Complementing cell lines

ABSTRACT

A packaging cell line that complements recombinant adenoviruses based on serotypes from subgroup B, preferably adenovirus type 35. The cell line is preferably derived from primary, diploid human cells that are transformed by adenovirus E1 sequences either operatively linked on one DNA molecule or located on two separate DNA molecules, the sequences being operatively linked to regulatory sequences enabling transcription and translation of encoded proteins. Also disclosed is a cell line derived from PER.C6 that expresses functional Ad35 E1B sequences. The Ad35-E1B sequences are driven by the E1B promoter or a heterologous promoter and terminated by a heterologous poly-adenylation signal. The cell lines are useful for producing recombinant adenoviruses designed for gene therapy and vaccination. The cell lines can also be used for producing human recombinant therapeutic proteins such as human growth factors and human antibodies. Also, the cell lines are useful for producing human viruses other than adenovirus such as influenza virus, herpes simplex virus, rotavirus, and measles virus.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of application U.S. Ser. No.10/002,750, filed Nov. 15, 2001, now U.S. Pat. No. 6,974,695, which is acontinuation-in-part of application Ser. No. 09/713,678, filed Nov. 15,2000, now U.S. Pat. No. 6,492,169, issued Dec. 10, 2002, the contents ofall of which are incorporated by this reference.

TECHNICAL FIELD

The invention relates to the field of biotechnology generally and, morespecifically, to adenoviral-based complementing cell lines.

SEQUENCE LISTING

Pursuant to 37 C.F.R. 1.821(e), applicants request that the compliantcomputer readable form Sequence Listing already submitted in theincorporated patent application U.S. Ser. No. 10/002,750, filed Nov. 15,2001 be used for this patent application. The paper copy of the“Sequence Listing” in this application is identical to the computerreadable copy filed for the patent application U.S. Ser. No. 10/002,750,filed Nov. 15, 2001.

BACKGROUND

Typically, vector and packaging cells have to be adapted to one anotherso that they have all the necessary elements, but they do not haveoverlapping elements that lead to replication-competent virus byrecombination. Therefore, the sequences necessary for propertranscription of the packaging construct may be heterologous regulatorysequences derived from, for example, other human adenovirus (Ad)serotypes, nonhuman adenoviruses, other viruses like, but not limitedto, SV40, hepatitis B virus (HBV), Rous Sarcoma Virus (RSV),cytomegalovirus (CMV), etc., or from higher eukaryotes such as mammals.In general, these sequences include a promoter, enhancer andpoly-adenylation sequences.

PER.C6 is an example of a cell line devoid of sequence overlap betweenthe packaging construct and the adenoviral vector (Fallaux et al.,1998). The PER.C6 cell line was deposited under ECACC deposit number96022940 under the provisions of the Budapest Treaty with the Centre forApplied Microbiology and Research Authority (European Collection ofAnimal Cell Cultures), Porton Down, Salisbury, Wiltshire SP4, OJG,United Kingdom, an International Depository Authority, on Feb. 29, 1996.Recombinant viruses based on subgroup C adenoviruses, such as Ad5 andAd2, can be propagated efficiently on these packaging cells. Generationand propagation of adenoviruses from other serotypes, like subgroup Bviruses, has proven to be more difficult on PER.C6 cells. However, asdescribed in EP Appln. 00201738.2, recombinant viruses based on subgroupB virus Ad35 can be made by co-transfection of an expression constructcontaining the Ad35 early region-1 sequences (Ad35-E1). Furthermore,Ad35-based viruses that are deleted for E1A sequences were shown toreplicate efficiently on PER.C6 cells. Thus, the E1A proteins of Ad5complement Ad35-E1A functions, whereas, at least part of the E1Bfunctions of Ad35 are necessary. This serotype specificity in E1Bfunctions was recently also described for Ad7 recombinant viruses. In anattempt to generate recombinant adenoviruses derived from subgroup Bvirus Ad7, Abrahamsen et al. (1997) were not able to generate E1-deletedviruses on 293 cells without contamination of wild-type (wt) Ad7.Viruses that were picked after plaque purification on 293ORF6 cells(Brough et al., 1996) were shown to have incorporated Ad7-E1B sequencesby nonhomologous recombination. Thus, efficient propagation of Ad7recombinant viruses proved possible only in the presence of Ad7-E1Bexpression and Ad5-E4-ORF6 expression. The E1B proteins are known tointeract with cellular, as well as viral, proteins (Bridge et al., 1993;White, 1995). Possibly, the complex formed between the E1B-55K proteinand E4-ORF6 which is necessary to increase mRNA export of viral proteinsand to inhibit export of most cellular mRNAs, is critical and in someway serotype-specific.

DISCLOSURE OF THE INVENTION

The invention provides new packaging cell lines capable of complementingrecombinant adenoviruses based on serotypes other than subgroup Cviruses, such as serotypes from subgroup B like adenovirus type 35.

In one aspect, the invention provides packaging cell lines capable ofcomplementing recombinant adenovirus based on a serotype of subgroup B,preferably of serotype 35. With the terms “based on or derived from anadenovirus” is meant that it utilizes nucleic acid corresponding tonucleic acid found in the serotype. The utilized nucleic acid may bederived by PCR cloning or other methods known in the art.

In one aspect, the new packaging cells are derived from primary, diploidhuman cells such as, but not limited to, primary human retinoblasts,primary human embryonic kidney cells or primary human amniocytes.Transfection of primary cells or derivatives thereof with the adenovirusE1A gene alone can induce unlimited proliferation (immortalization), butdoes not result in complete transformation. However, expression of E1Ain most cases results in induction of programmed cell death (apoptosis),and occasionally immortalization is obtained (Jochemsen et al., 1987).Co-expression of the E1B gene is required to prevent induction ofapoptosis and for complete morphological transformation to occur(reviewed in White, 1995). Therefore, in one aspect of the invention,primary human cells or derivatives thereof are transformed by expressionof adenovirus E1 proteins of a subgroup other than subgroup C,preferably subgroup B, more preferably adenovirus type 35. The combinedactivity of the E1A and E1B proteins establishes indefinite growth ofthe cells and enables complementation of recombinant adenoviruses.

The complete morphological transformation of primary cells by adenovirusE1 genes is the result of the combined activities of the proteinsencoded by the E1A and E1B regions. The roles of the different E1proteins in lytic infection and in transformation have been studiedextensively (reviewed in Zantema and van der Eb, 1995; White, 1995,1996). The adenovirus E1A proteins are essential for transformation ofprimary cells. The E1A proteins exert this effect through directinteraction with a number of cellular proteins that are involved inregulation of transcription. These include the pRB family of proteins,p300/CBP and TATA binding protein. In addition to this E1A increases thelevel of p53 protein in the cells. In the absence of adenovirus E1Bactivity the rise in p53 levels leads to the induction of apoptosis.Both proteins encoded by the E1B region counteract the induction ofapoptosis although by different mechanisms. E1B-21K seems to counteractapoptosis in a manner similar to Bcl-2 via interaction with the effectorproteins downstream in the apoptosis pathway (Han et al., 1996), whereasE1B-55K functions through direct interaction with p53. Importantly, themolecular mechanism by which the E1B-55K proteins of Ad2 and 5 (subgroupC) and Ad12 (subgroup A) function in the ability to neutralize p53 maydiffer. Whereas Ad5 E1B-55K binds p53 strongly and the complex localizesto the cytoplasm, Ad12 E1B-55K binds p53 weakly and both proteins arelocalized in the nucleus (Zantema et al., 1985; Grand et al., 1999).Both proteins, however, inhibit the transactivation of other genes byp53 (Yew and Berk, 1992).

In rodent cells, the activity of E1A together with either E1B-21K or 55Kis sufficient for full transformation although expression of both E1Bproteins together is twice as efficient (Rao et al., 1992). In humancells however, the activity of the E1B-55K protein seems to be moreimportant given the observation that E1B-55K is indispensable for theestablishment of transformed cells (Gallimore, 1986).

Example 6 hereof describes the generation of pIG270. In this construct,the Ad35-E1 genes are expressed from the hPGK promoter and transcriptionis terminated by the HBVpA. The hPGK promoter constitutes a HincII-EcoRIfragment of the promoter sequence described by Singer-Sam et al. (1984).The HBVpA is located in a BamHI-BglII fragment of the Hepatitis B virusgenome (Simonsen and Levinson, 1983; see also Genbank HBV-AF090841). Asmentioned before, the promoter and polyadenylation sequences of the E1expression constructs described in this invention may be derived fromother sources without departing from the invention. Also, otherfunctional fragments of the hPGK and HBVpA sequences mentioned hereinmay be used.

The functionality of pIG270 was shown by transformation of primary BabyRat Kidney cells (BRK). Comparison with an equivalent Ad5-E1 expressionconstruct taught that Ad35-E1 genes were less efficient in transformingthese cells. The same has been found for the E1 genes of Ad12 (Bernardset al., 1982).

It is unclear which E1 protein(s) determine(s) the difference intransformation efficiency of E1 sequences observed for adenoviruses fromdifferent subgroups. In the case of Ad12, transfection studies withchimeric E1A/E1B genes suggested that the efficiency of transformationof BRK cells was determined by the E1A proteins (Bernards et al., 1982).The E1B-55K protein is shown injra to contain serotype-specificfunctions necessary for complementation of E1-deleted adenoviruses. Ifthese functions are related to the regulation of mRNA distribution oranother late viral function, it is unlikely that these are involved inthe transformation efficiency.

Analysis of functional domains in the Ad2 or Ad5 E1B-55K proteins usinginsertion mutants have revealed that functions related to viralreplication, late protein synthesis and host protein shut-off are notconfined to specific domains but are distributed along the protein (Yewet al., 1990). Using the same set of mutants, the domains important forinteraction with p53 and E4-Orf6 were found to be more restricted. Inaddition to one common binding region (amino acids 262 to 326), p53binding was affected by mutations at aa 180 and E4-Orf6 binding wasaffected by mutations at aa 143 (Yew and Berk, 1992; Rubenwolf et al.,1997).

Altogether these results indicate that it is difficult to separate theE1B-55K functions related to transformation (p53 binding) and lateprotein synthesis (Orf6 binding).

The invention discloses new E1 constructs that combine the highefficiency of transformation of one serotype with the serotype-specificcomplementation function of another serotype. These new constructs areused to transform primary human embryonic retinoblast cells and humanamniocytes.

In another aspect of the invention, the transforming E1 sequences arederived from different serotypes. As disclosed in European Patentapplication 00201738.2, Ad35E1 sequences are capable of transformingBaby Rat Kidney (BRK) cells, albeit with a lower efficiency than thatseen with Ad5-E1 sequences. This was also observed for E1 sequences fromAd12 (Bemards et al., 1982). Therefore, in this aspect of the invention,primary diploid human cells or derivatives thereof are transformed withchimeric E1 construct that consists of part of the E1 sequences of aserotype that enables efficient transformation of primary human cells orderivatives thereof and part of the E1 sequences of another serotypewhich E1 sequences provide the serotype-specific E1B function(s) thatenable(s) efficient propagation of E1-deleted viruses of that serotype.In a preferred embodiment of this aspect of the invention, the E1Aregion is derived from a subgroup C adenovirus like, but not limited to,Ad5, and the E1B coding sequences are derived from an alternativeadenovirus, more particularly from an adenovirus of subgroup B, evenmore particularly from adenovirus type 35. E1B-21K coding sequences mayalso be chimeric comprising both subgroup C and subgroup B codingsequences. Preferably, all or most of E1B-21K comprises subgroup Ccoding sequences. In a more preferred embodiment, the E1A codingsequences and the E1B-21K coding sequences are derived from a subgroup Cadenovirus, like, but not limited to, Ad5. In one embodiment the cellfurther comprises E1B55k coding sequences that are, preferably, as faras not overlapping with the 21K coding sequences derived from anadenovirus of subgroup B, more particularly from adenovirus type 35. Inan even more preferred embodiment, all E1 coding sequences are derivedfrom a subgroup C adenovirus, like but not limited to Ad5, except for atleast the part of the E1B-55K coding sequences that are necessary forserotype-specific complementation of an alternative adenovirus subgroup,more particularly adenovirus subgroup B, even more particular adenovirustype 35. The invention also provides a packaging cell line wherein theprimary, diploid human cells or derivatives thereof have beentransformed with a chimeric adenovirus E1 construct comprising part of afirst adenovirus E1 coding sequence of a first adenovirus serotype thatenables efficient transformation of primary human cells and derivativesthereof; and part of a second adenovirus E1 coding sequence of a secondadenovirus serotype, wherein the second adenovirus E1 coding sequenceprovides the serotype-specific adenovirus E1B function(s) that enable(s)efficient propagation of recombinant adenovirus E1-deleted viruses ofthe second adenovirus serotype. Preferably, the first adenovirusserotype is a subgroup C adenovirus and the second adenovirus serotypeis a subgroup B adenovirus, more particular adenovirus type 35. In oneembodiment the packing cell line of the invention comprises bovineadenovirus E1B-55k. Such a bovine E1B-55k expressing cell line isparticularly suited for obtaining high yields of a complemented bovinerecombinant adenovirus.

The primary diploid human cells or derivatives thereof are transformedby adenovirus E1 sequences, either operatively linked on one DNAmolecule or located on two separate DNA molecules. In the latter case,one DNA molecule carries at least part of the E1 sequences of theserotype-enabling efficient transformation and the second DNA moleculecarries at least part of the sequences necessary for serotype-specificcomplementation. Also provided is a hybrid construct includingE1-sequences of the serotype enabling efficient transformation andE1-sequences of another serotype necessary for serotype-specificcomplementation. The sequences providing serotype specificcomplementation may of course also contain further activitiescontributing to transformation. Preferably, the sequences enablingefficient transformation comprise E1A. Preferably, the sequences and thesequences necessary for serotype specific complementation preferablycomprise E1B sequences. More preferably, the sequences enablingefficient transforming comprise E1A and E1B-21K sequences and thesequences necessary for serotype specific complementation compriseE1B-55K sequences. Also provided are cells transformed by such hybridconstruct. Such cells can favorably be used for the propagation ofrecombinant E1 deleted adenovirus of another serotype. Of course, it isalso possible to provide both functions of E1 sequences on separateconstructs. In all aspects, the sequences are operatively linked toregulatory sequences enabling transcription and translation of theencoded proteins. Preferably, a packaging cell of the invention furthercomprises a DNA encoding at least E4-orf6 of an adenovirus of subgroupB, preferably adenovirus serotype 35. Preferably, the E4-orf6 is derivedfrom the other serotype. Preferably, the cell comprises E1B-55K andE4-orf6 of the same serotype as the recombinant vector to bepropagated/complemented or otherwise produced.

In another aspect of the invention, new packaging cells are describedthat are derived from PER.C6 (ECACC deposit number 96022940; Fallaux etal., 1998) and contain Ad35-E1 sequences integrated into their genome.These Ad35-E1 sequences are present in a functional expression cassette,but preferably do not contain sequences overlapping with sequencespresent in the recombinant viral vector. Preferably, the functionalexpression cassette consists of a heterologous promoter andpoly-adenylation signal functionally linked to Ad35-E1 sequences. Morespecifically, the Ad35-E1 coding sequences are functionally linked tothe human phosphoglycerate gene promoter (hPGK) and hepatitus B viruspoly-adenylation signal (HBV-pA). Preferably, Ad35-E1 coding sequencescomprise the coding regions of the E1A proteins and the E1B promotersequences linked to E1B coding sequences up to and including the stopcodon of the E1B 55K protein. More preferably, the Ad35-E1 sequencescomprise nucleotide 468 to nucleotide 3400 of the Ad35 wt sequence. Tobe able to select for transfected cells, a dominant selection markerlike, but not limited to, the neo^(r) gene has to be incorporated on theexpression vector or the Ad35 expression vector is cotransfected with aseparate expression vector mediating expression of the selection marker.In both cases, the selection marker becomes integrated in the cellulargenome. Other Ad5-E1 transformed cell lines like 293 (Graham et al.,1977) and 911 (Fallaux et al., 1996) or established human cell lineslike A549 cells may be used without departing from the presentinvention.

In another aspect of the invention, PER.C6-derived cells are describedthat express functional Ad35-E1B sequences. In one embodiment, theAd35-E1B coding sequences are driven by the E1B promoter and terminatedby a heterologous poly-adenylation signal like, but not limited to, theHBVpA. In a preferred embodiment, the Ad35-E1B coding sequences aredriven by a heterologous promoter like, but not limited to, the hPGKpromoter or Elongation Factor-1α (EF-1α) promoter and terminated by aheterologous pA signal like, but not limited to, the HBVpA. TheseAd35-E1B sequences preferably comprise the coding regions of the E1B-21Kand the E1B-55K proteins located between nucleotides 1611 and 3400 ofthe wild-type (wt) Ad35 sequence. More preferably, the Ad35-E1Bsequences comprise nucleotides 1550 to 3400 of the wt Ad35 sequence. Inan even more preferred embodiment, the E1B sequences comprise the codingsequences of the E1B-55K gene located between nucleotides 1916 and 3400of the wt Ad35 sequence. In an even more preferred embodiment apackaging cell line or a cell line of the invention lacks a functionalcoding sequence for E1B 21k. Such cell lines, in general, producesignificantly more recombinant adenovirus than E1B21K positive celllines.

The invention further provides a method for complementing a recombinantadenovirus comprising providing a packaging cell line or a cell lineaccording to the invention, with the recombinant adenovirus andculturing the cell to allow for complementation. In a preferredembodiment the method further comprises harvesting complementedrecombinant adenovirus. Preferably, the recombinant adenovirus isderived from adenovirus subgroup B. More preferably, the recombinantadenovirus is derived from adenovirus serotype 35.

In another aspect, the invention provides a recombinant adenovirusobtained by a method of the invention or with a packaging cell of theinvention. Such an adenovirus can be obtained essentially free fromcontaminating wild type adenovirus, or replication competent adenovirus.Such recombinant adenovirus preparations are very suited foradministration of therapeutic sequences to somatic tissues in vivo infor instance a gene therapeutic setting. Preferred are recombinantadenoviruses comprising a deletion of nucleic acid encoding at least oneE1-region protein. Preferably, such adenovirus further comprises adeletion of nucleic acid encoding at least one E3-region protein.Preferably, such adenovirus further comprises a deletion of nucleic acidencoding at least one E4-region protein. Preferably, such adenovirusfurther comprises a deletion of nucleic acid encoding at least oneE4-Orf6 protein. For this reason, the invention also provides the use ofa recombinant adenovirus of the invention for the preparation of amedicament.

With the term E1B-55K protein as used herein, is meant the proteinencoded by the E1B-region in an adenovirus serotype having a similarfunction in the serotype as provided by the E1B-55K protein Ad5.

With the term E1B-21K protein as used herein, is meant the proteinenclosed by the E1B-region in an adenovirus serotype having a similarfunction in the serotype as provided by the E1B-19K protein of Ad5. Thesame terminology applies for the sequences encoding these proteins. Whenreferring to Ad35-E1 sequences from a specified nucleotide to nucleotide3400 is meant “up to and including nucleotide 3400.”

The cell lines of this invention are useful for, among other things,producing recombinant adenoviruses designed for gene therapy andvaccination. The cell lines, being derived from cells of human origin,are also useful for the production of human recombinant therapeuticproteins like, but not limited to human growth factors, humanantibodies. In addition the cell lines are useful for the production ofhuman viruses other than adenovirus like, but not limited to, influenzavirus, herpes simplex virus, rotavirus, measles virus.

A preferred derivative of primary, diploid human cells is the PER.C6cell line (ECACC deposit number 960022940).

It is within the skills of the artisan to provide for proteins having asimilar function in kind as the adenovirus E1 protein referred to inthis document. For instance a functional part may be provided and/or aderivative may be provided with a similar function in kind, notnecessarily in amount.

Such parts and derivatives are considered to be part of the invention,in as far as similar transforming/complementing and/or serotypespecificity function is provided in kind, not necessarily in amount.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1: Bar graph showing the percentage of serum samples positive forneutralization for each human wt adenovirus tested (see, Example 1 fordescription of the neutralization assay).

FIG. 2: Graph showing absence of correlation between the VP/CCID50 ratioand the percentage of neutralization.

FIG. 3: Bar graph presenting the percentage sera samples that showneutralizing activity to a selection of adenovirus serotypes. Sera werederived from healthy volunteers from Belgium and the UK.

FIG. 4: Bar graph presenting the percentage sera samples that showneutralizing activity to adenovirus serotypes 5, 11, 26, 34, 35, 48 and49. Sera were derived from five different locations in Europe and theUnited States.

FIG. 5: Map of pAdApt35IP1.

FIG. 6: Schematic representation of the steps undertaken to constructpWE.Ad35.pIX-rITR.

FIG. 7: Map of pWE.Ad35.pIX-rITR.

FIG. 8: Map of pRSV.Ad35-E1.

FIG. 9 Map of pPGKneopA

FIG. 10: Map of pRSV-Pneo.

FIG. 11: Map of pRSVhbv.Neo.

FIG. 12: Map of pIG.E1.E1B.

FIG. 13: Map of pIG135.

FIG. 14: Map of pIG270.

FIG. 15: Map of pBr.Ad35.leftITR-pIX.

FIG. 16: Map of pBr.Ad35.leftITR-pIXdE1A.

FIG. 17: Map of pBr.Ad35.d21K.

FIG. 18: Map of pBr.Ad35.d55K1.

FIG. 19: Map of pBr.Ad35DdSM.

FIG. 20: Schematic representation of Ad35-E1A/E1B deletion constructs.

FIG. 21: Map of pIG.35BL.

FIG. 22: Map of pRSVneo4.

FIG. 23: Map of pIG35Bneo.

FIG. 24: Map of pIG35.55K.

FIG. 25: Map of pIG535.

FIG. 26: Map of pIG635.

FIG. 27: Map of pIG735.

FIG. 28: Map of pCC271.

FIG. 29: Map of pCC535s.

FIG. 30: Map of pCR535E1B.

FIG. 31: Map of pCC2155s.

FIG. 32: Map of pCC536s.

FIG. 33: Map of pIG536.

FIG. 34: Map of pBr.Ad35.PRn.

FIG. 35: Map of pBr.Ad35.PRnΔE3.

FIG. 36: Map of pWE.Ad35.pIX-rITRΔE3.

FIG. 37: Alignment of E1B-21K amino acid sequences in pCC536s (SEQ IDNO:45), wtAd5 (SEQ ID NO:46) and wtAd35 (SEQ ID NO:47) (A) and E1B-55Kamino acid sequences in pCC536s (SEQ ID NO:48), wtAd5 (SEQ ID NO:49) andwtAd35 (SEQ ID NO:50) (B).

The invention is further explained by the use of the followingillustrative examples.

EXAMPLES Example 1

A High Throughput Assay for the Detection of Neutralizing Activity inHuman Serum

To enable screening of a large amount of human sera for the presence ofneutralizing antibodies against all adenovirus serotypes, an automated96-wells assay was developed.

Human Sera

A panel of 100 individuals was selected. Volunteers (50% male, 50%female) were healthy individuals between ages 20 and 60 years old withno restriction for race. All volunteers signed an informed consent form.People professionally involved in adenovirus research were excluded.

Approximately 60 ml blood was drawn in dry tubes. Within two hours aftersampling, the blood was centrifuged at 2500 rpm for 10 minutes.Approximately 30 ml serum was transferred to polypropylene tubes andstored frozen at −20° C. until further use.

Serum was thawed and heat-inactivated at 56° C. for 10 minutes and thenaliquoted to prevent repeated cycles of freeze/thawing. Part was used tomake five steps of twofold dilutions in medium (DMEM, Gibco BRL) in aquantity large enough to fill out approximately 70 96-well plates.Aliquots of undiluted and diluted sera were pipetted in deep well plates(96-well format) and using a programmed platemate dispensed in 100 μlaliquots into 96-well plates. The plates were loaded with eightdifferent sera in duplo (100 μl/well) according to the scheme below:

S1/2 S1/4 S1/8 S1/ S1/ S5/2 S5/4 S5/8 S5/ S5/32 — — 16 32 16 S1/2 S1/4S1/8 S1/ S1/ S5/2 S5/4 S5/8 S5/ S5/32 — — 16 32 16 S2/2 S2/4 S2/8 S2/S2/ S6/2 S6/4 S6/8 S6/ S6/32 — — 16 32 16 S2/2 S2/4 S2/8 S2/ S2/ S6/2S6/4 S6/8 S6/ S6/32 — — 16 32 16 S3/2 S3/4 S3/8 S3/ S3/ S7/2 S7/4 S7/8S7/ S7/32 — — 16 32 16 S3/2 S3/4 S3/8 S3/ S3/ S7/2 S7/4 S7/8 S7/ S7/32 —— 16 32 16 S4/2 S4/4 S3/8 S3/ S3/ S8/2 S8/4 S8/8 S8/ S8/32 — — 16 32 16S4/2 S4/4 S3/8 S3/ S3/ S8/2 S8/4 S8/8 S8/ S8/32 — — 16 32 16Where S1/2 to S8/2 in columns 1 and 6 represent 1× diluted sera andSx/4, Sx/8, Sx/16 and Sx/32 the twofold serial dilutions. The lastplates also contained four wells filled with 100 μl fetal calf serum asa negative control. Plates were kept at −20° C. until further use.Preparation of Human Adenovirus Stocks

Prototypes of all known human adenoviruses were inoculated on T25 flasksseeded with PER.C6 cells (Fallaux et al., 1998) and harvested upon fullCPE. After freeze/thawing, 1-2 ml of the crude lysates were used toinoculate a T80 flask with PER.C6 and virus was harvested at full CPE.The timeframe between inoculation and occurrence of CPE, as well as theamount of virus needed to re-infect a new culture, differed betweenserotypes. Adenovirus stocks were prepared by freeze/thawing and used toinoculate 3-4 T175 cm² three-layer flasks with PER.C6 cells. Uponoccurrence of CPE, cells were harvested by tapping the flask, pelletedand virus was isolated and purified by a two-step CsCl gradient asfollows. Cell pellets were dissolved in 50 ml 10 mM NaPO₄ buffer (pH7.2) and frozen at −20° C. After thawing at 37° C., 5.6 ml sodiumdeoxycholate (5% w/v) was added. The solution was mixed gently andincubated for 5-15 minutes at 37° C. to completely lyse the cells. Afterhomogenizing the solution, 1875 μl 1M MgCl₂ was added. After theaddition of 375 μl DNAse (10 mg/ml), the solution was incubated for 30minutes at 37° C. Cell debris was removed by centrifugation at 1880×gfor 30 minutes at RT without brake. The supernatant was subsequentlypurified from proteins by extraction with FREON (3×). The clearedsupernatant was loaded on a 1M Tris/HCl buffered cesium chloride blockgradient (range: 1.2/1.4 g/ml) and centrifuged at 21000 rpm for 2.5hours at 10° C. The virus band is isolated after which a secondpurification using a 1M Tris/HCl buffered continues gradient of 1.33g/ml of cesium chloride was performed. The virus was then centrifugedfor 17 hours at 55000 rpm at 10° C. The virus band is isolated andsucrose (50% w/v) is added to a final concentration of 1%. Excess cesiumchloride is removed by dialysis (three times 1 hr at RT) in dialysisslides (Slide-a-lizer, cut off 10000 kDa, Pierce, USA) against 1.5 literPBS supplemented with CaCl₂ (0.9 mM), MgCl₂ (0.5 mM) and an increasingconcentration of sucrose (1, 2, 5%). After dialysis, the virus isremoved from the slide-a-lizer after which it is aliquoted in portionsof 25 and 100 μl upon which the virus is stored at −85° C.

To determine the number of virus particles per milliliter, 50 μl of thevirus batch is run on a high-pressure liquid chromatograph (HPLC) asdescribed by Shabram et al (1997). Viruses were eluted using a NaClgradient ranging from 0 to 600 mM. As depicted in Table I, the NaClconcentration by which the viruses were eluted differed significantlyamong serotypes.

Most human adenoviruses replicated well on PER.C6 cells with a fewexceptions. Adenovirus type 8 and 40 were grown on 911-E4 cells (He etal., 1998). Purified stocks contained between 5×10¹⁰ and 5×10¹² virusparticles/ml (VP/ml; see table I).

Titration of Purified Human Adenovirus Stocks

Adenoviruses were titrated on PER.C6 cells to determine the amount ofvirus necessary to obtain full CPE in five days, the length of theneutralization assay. Hereto, 100 μl medium was dispensed into each wellof 96-well plates. 25 μl of adenovirus stocks pre-diluted 10⁴, 10⁵, 10⁶or 10⁷ times were added to column 2 of a 96-well plate and mixed bypipetting up and down 10 times. Then 25 μl was brought from column 2 tocolumn 3 and again mixed. This was repeated until column 11, after which25 μl from column 11 was discarded. This way, serial dilutions in stepsof 5 were obtained starting off from a pre-diluted stock. Then 3×10⁴PER.C6 cells (ECACC deposit number 96022940) were added in a 100 μlvolume and the plates were incubated at 37° C., 5% CO₂ for five or sixdays. CPE was monitored microscopically. The method of Reed and Muenschwas used to calculate the cell culture-inhibiting dose 50% (CCID50).

In parallel, identical plates were set up that were analyzed using theMTT assay (Promega). In this assay, living cells are quantified bycalorimetric staining. Hereto, 20 μl MTT (7.5 mgr/ml in PBS) was addedto the wells and incubated at 37° C., 5% CO₂ for two hours. Thesupernatant was removed and 100 μl of a 20:1 isopropanol/triton-X100solution was added to the wells. The plates were put on a 96-well shakerfor 3-5 minutes to solubilize the precipitated staining. Absorbance wasmeasured at 540 nm and at 690 nm (background). By this assay, wells withproceeding CPE or full CPE can be distinguished.

Neutralization Assay

96-well plates with diluted human serum samples were thawed at 37° C.,5% CO₂. Adenovirus stocks diluted to 200 CCID50 per 50 μl were preparedand 50 μl aliquots were added to columns 1-11 of the plates with serum.Plates were incubated for 1 hour at 37° C., 5% CO₂. Then, 50 μl PER.C6cells at 6×10⁵/ml were dispensed in all wells and incubated for 1 day at37° C., 5% CO₂. Supernatant was removed using fresh pipette tips foreach row and 200 μl fresh medium was added to all wells to avoid toxiceffects of the serum. Plates were incubated for another 4 days at 37°C., 5% CO₂. In addition, parallel control plates were set up in duplo,with diluted positive control sera generated in rabbits and specific foreach serotype to be tested in rows A and B and with negative controlserum (FCS) in rows C and D. Also, in each of the rows E-H, a titrationwas performed as described above with steps of five times dilutionsstarting with 200 CCID50 of each virus to be tested. On day 5, one ofthe control plates was analyzed microscopically and with the MTT assay.The experimental titer was calculated from the control titration plateobserved microscopically. If CPE was found to be complete, i.e., thefirst dilution in the control titration experiment analyzed by MTT showsclear cell death, all assay plates were processed. If not, the assay wasallowed to proceed for one or more days until full CPE was apparent,after which all plates were processed. In most cases, the assay wasterminated at day 5. For Ad1, 5, 33, 39, 42 and 43 the assay was leftfor six days and for Ad2 for eight days.

A serum sample is regarded as “non-neutralizing” when, at the highestserum concentration, a maximum protection of 40% is seen compared tocontrols without serum.

The results of the analysis of 44 prototype adenoviruses against serumfrom 100 healthy volunteers are shown in FIG. 1. As expected, thepercentage of serum samples that contained neutralizing antibodies toAd2 and Ad5 was very high. This was also true for most of the lowernumbered adenoviruses. Surprisingly, none of the serum samples containedneutralizing antibodies to Ad35. Also, the number of individuals withneutralizing antibody titers to the serotypes 26, 34 and 48 was verylow. Therefore, recombinant E1-deleted adenoviruses based on Ad35 or oneof the other above-mentioned serotypes have an important advantagecompared to recombinant vectors based on Ad5 with respect to clearanceof the viruses by neutralizing antibodies.

Also, Ad5-based vectors that have parts of the capsid proteins involvedin immunogenic response of the host replaced by the corresponding partsof the capsid proteins of Ad35 or one of the other serotypes will beless, or even not, neutralized by the vast majority of human sera.

As can be seen in Table I, the VP/CCID50 ratio calculated from the virusparticles per ml and the CCID50 obtained for each virus in theexperiments was highly variable and ranged from 0.4 to 5 log. This isprobably caused by different infection efficiencies of PER.C6 cells andby differences in replication efficiency of the viruses. Furthermore,differences in batch qualities may play a role. A high VP/CCID50 ratiomeans that more viruses were put in the wells to obtain CPE in 5 days.As a consequence, the outcome of the neutralization study might bebiased since more inactive virus particles could shield the antibodies.To check whether this phenomenon had taken place, the VP/CCID50 ratiowas plotted against the percentage of serum samples found positive inthe assay (FIG. 2). The graph clearly shows that there is no negativecorrelation between the amount of viruses in the assay andneutralization in serum.

Example 2

The Prevalence of Neutralizing Activity (NA) to Ad35 is Low in HumanSera from Different Geographic Locations

In Example 1, the analysis of neutralizing activity (“NA”) in human serafrom one location in Belgium was described. Strikingly, of a panel of 44adenovirus serotypes tested, one serotype, Ad35, was not neutralized inany of the 100 sera assayed. In addition, a few serotypes, Ad26, Ad34and Ad48 were found to be neutralized in 8%, or less, of the seratested. This analysis was further extended to other serotypes ofadenovirus not previously tested and, using a selection of serotypesfrom the first screen, was also extended to sera from differentgeographic locations.

Hereto, adenoviruses were propagated, purified and tested forneutralization in the CPE-inhibition assay as described in Example 1.Using the sera from the same batch as in Example 1, adenovirus serotypes7B, 11, 14, 18 and 44/1876 were tested for neutralization. These viruseswere found to be neutralized in, respectively, 59, 13, 30, 98 and 54% ofthe sera. Thus, of this series, Ad11 is neutralized with a relativelylow frequency.

Since it is known that the frequency of isolation of adenovirusserotypes from human tissue, as well as the prevalence of NA toadenovirus serotypes, may differ on different geographic locations, wefurther tested a selection of the adenovirus serotypes against sera fromdifferent places. Human sera were obtained from two additional places inEurope (Bristol, UK and Leiden, NL) and from two places in the UnitedStates (Stanford, Calif. and Great Neck, N.Y.). Adenoviruses that werefound to be neutralized in 20% or less of the sera in the first screen,as well as Ad2, Ad5, Ad27, Ad30, Ad38, Ad43, were tested forneutralization in sera from the UK. The results of these experiments arepresented in FIG. 3. Adenovirus serotypes 2 and 5 were again neutralizedin a high percentage of human sera. Furthermore, some of the serotypesthat were neutralized in a low percentage of sera in the first screenare neutralized in a higher percentage of sera from the UK, for example,Ad26 (7% vs. 30%), Ad28 (13% vs. 50%), Ad34 (5% vs. 27%) and Ad48 (8%vs. 32%). Neutralizing activity against Ad11 and Ad49 that were found ina relatively low percentage of sera in the first screen, are found in aneven lower percentage of sera in this second screen (13% vs. 5% and 20%vs. 11%, respectively). Serotype Ad35 that was not neutralized in any ofthe sera in the first screen, was now found to be neutralized in a lowpercentage (8%) of sera from the UK. The prevalence of NA in human serafrom the UK is the lowest to serotypes Ad11 and Ad35.

For further analysis, sera was obtained from two locations in the US(Stanford, Calif. and Great Neck, N.Y.) and from The Netherlands(Leiden). FIG. 4 presents an overview of data obtained with these seraand the previous data. Not all viruses were tested in all sera, exceptfor Ad5, Ad11 and Ad35. The overall conclusion from this comprehensivescreen of human sera is that the prevalence of neutralizing activity toAd35 is the lowest of all serotypes throughout the western countries: onaverage 7% of the human sera contain neutralizing activity (5 differentlocations). Another B-group adenovirus, Ad11 is also neutralized in alow percentage of human sera (average 11% in sera from 5 differentlocations). Adenovirus type 5 is neutralized in 56% of the human seraobtained from 5 different locations. Although not tested in all sera,D-group serotype 49 is also neutralized with relatively low frequency insamples from Europe and from one location of the US (average 14%).

In the herein described neutralization experiments, a serum is judgednon-neutralizing when, in the well with the highest serum concentration,the maximum protection of CPE is 40% compared to the controls withoutserum. The protection is calculated as follows:

${1\%\mspace{14mu}{protection}} = {\frac{{{OD}\mspace{14mu}{corresponding}\mspace{14mu}{well}} - {{OD}\mspace{14mu}{virus}\mspace{14mu}{control}}}{{{OD}\mspace{14mu}{non}\text{-}{infected}\mspace{14mu}{control}} - {{OD}\mspace{14mu}{virus}\mspace{14mu}{control}}} \times 100\%}$

As described in Example 1, the serum is plated in five differentdilutions ranging from 4× to 64× diluted. Therefore, it is possible todistinguish between low titers (i.e., neutralization only in the highestserum concentrations) and high titers of NA (i.e., also neutralizationin wells with the lowest serum concentration). Of the human sera used inour screen that were found to contain neutralizing activity to Ad5, 70%turned out to have high titers, whereas, of the sera that contained NAto Ad35, only 15% had high titers. Of the sera that were positive for NAto Ad11, only 8% had high titers. For Ad49, this was 5%. Therefore, notonly is the frequency of NA to Ad35, Ad11 and Ad49 much lower ascompared to Ad5, but of the sera that do contain NA to these viruses,the vast majority have low titers. Adenoviral vectors based on Ad11,Ad35 or Ad49 have, therefore, a clear advantage over Ad5-based vectorswhen used as gene therapy vehicles or vaccination vectors in vivo or inany application where infection efficiency is hampered by neutralizingactivity.

In the following examples, the construction of a vector system for thegeneration of safe, RCA-free Ad35-based vectors is described.

Example 3

Sequence of the Human Adenovirus Type 35

Ad35 viruses were propagated on PER.C6 cells and DNA was isolated asfollows: To 100 μl of virus stock (Ad35: 3.26×10¹² VP/ml), 10 μl 10×DNAse buffer (130 mM Tris-HCl pH7.5; 1,2 M CaCl₂; 50 mM MgCl₂) wasadded. After addition of 10 μl 10 mgr/ml DNAse I (Roche Diagnostics),the mixture was incubated for 1 hr. at 37° C. Following addition of 2.5μl 0.5M EDTA, 3.2 μl 20% SDS and 1.5 μl ProteinaseK (Roche Diagnostics;20 mgr/ml), samples were incubated at 50° C. for 1 hr. Next, the viralDNA was isolated using the GENECLEAN spin kit (BIO 101 Inc.) accordingto the manufacturer's instructions. DNA was eluted from the spin columnwith 25 μl sterile MilliQ water. The total sequence was generated byQiagen Sequence Services (Qiagen GmbH, Germany). Total viral DNA wassheared by sonification and the ends of the DNA were made blunt by T4DNA polymerase. Sheared blunt fragments were size fractionated onagarose gels and gel slices corresponding to DNA fragments of 1.8 to 2.2kb were obtained. DNA was purified from the gel slices by the QIAquickgel extraction protocol and subcloned into a shotgun library of pUC19plasmid cloning vectors. An array of clones in 96-well plates coveringthe target DNA 8 (+/−2) times was used to generate the total sequence.Sequencing was performed on Perkin-Elmer 9700 thermocyclers using BigDye Terminator chemistry and AmpliTaq FS DNA polymerase followed bypurification of sequencing reactions using QIAGEN DyeEx 96 technology.Sequencing reaction products were then subjected to automated separationand detection of fragments on ABI 377 XL 96 lane sequencers. Initialsequence results were used to generate a contiguous sequence and gapswere filled in by primer walking reads on the target DNA or by directsequencing of PCR products. The ends of the virus turned out to beabsent in the shotgun library, most probably due to cloning difficultiesresulting from the amino acids of pTP that remain bound to the ITRsequences after proteinase K digestion of the viral DNA. Additionalsequence runs on viral DNA solved most of the sequence in those regions,however, it was difficult to obtain a clear sequence of the mostterminal nucleotides. At the 5′ end the sequence portion obtained was5′-CCAATAATATACCT-3′ (SEQ ID NO:1) while at the 3′ end, the obtainedsequence portion was 5′-AGGTATATTATTGATGATGGG-3′ (SEQ ID NO:2). Mosthuman adenoviruses have a terminal sequence 5′-CATCATCAATAATATACC-3′(SEQ ID NO:3). In addition, a clone representing the 3′ end of the Ad35DNA obtained after cloning the terminal 7 kb Ad35 EcoRI fragment intopBr322 also turned out to have the typical CATCATCAATAAT . . . sequence.Therefore, Ad35 may have the typical end sequence and the differencesobtained in sequencing directly on the viral DNA are due to artifactscorrelated with run-off sequence runs and the presence of residual aminoacids of pTP.

The total sequence of Ad35 with corrected terminal sequences is given inSEQ ID NO:44. Based sequence homology with Ad5 (Genbank # M72360) andAd7 (partial sequence Genbank # X03000) and on the location of openreading frames, the organization of the virus is identical to thegeneral organization of most human adenoviruses, especially the subgroupB viruses. The total length of the genome is 34,794 basepairs.

Example 4

Construction of a Plasmid-Based Vector System to Generate RecombinantAd35-Based Viruses

A functional plasmid-based vector system to generate recombinantadenoviral vectors comprises the following components:

1. An adapter plasmid comprising a left ITR and packaging sequencesderived from Ad35 and at least one restriction site for insertion of aheterologous expression cassette and lacking E1 sequences. Furthermore,the adapter plasmid contains Ad35 sequences 3′ from the E1B codingregion including the pIX promoter and coding sequences enough to mediatehomologous recombination of the adapter plasmid with a second nucleicacid molecule.

2. A second nucleic acid molecule, comprising sequences homologous tothe adapter plasmid, and Ad35 sequences necessary for the replicationand packaging of the recombinant virus, that is, early, intermediate andlate genes that are not present in the packaging cell.

3. A packaging cell providing at least functional E1 proteins capable ofcomplementing the E1 function of Ad35.

Other methods for generating recombinant adenoviruses on complementingpackaging cells are known in the art and may be applied to Ad35 viruseswithout departing from the invention. As an example, the construction ofa plasmid-based system, as outlined above, is described in detail below.

1) Construction of Ad35 Adapter Plasmids

The adapter plasmid pAdApt (described in International PatentPublication WO99/55132) was first modified to obtain adapter plasmidsthat contain extended polylinkers and that have convenient uniquerestriction sites flanking the left ITR and the adenovirus sequence atthe 3′ end to enable liberation of the adenovirus insert from plasmidvector sequences. Construction of these plasmids is described below indetail:

1) Construction of Ad35 Adapter Plasmids

Adapter plasmid pAdApt was digested with SalI and treated with ShrimpAlkaline Phosphatase to reduce religation. A linker, composed of thefollowing two phosphorylated and annealed oligos: ExSalPacF 5′-TCG ATGGCA AAC AGC TAT TAT GGG TAT TAT GGG TTC GAA TTA ATT AA-3′ (SEQ ID NO:4)and ExSalPacR 5′-TCG ATT AAT TAA TTC GAA CCC ATA ATA CCC ATA ATA GCT GTTTGC CA-3′ (SEQ ID NO:5) was directly ligated into the digestedconstruct, thereby replacing the SalI restriction site by Pi-PspI, Swaland PacI. This construct was designated pADAPT+ExSalPac linker.Furthermore, part of the left ITR of pAdApt was amplified by PCR usingthe following primers: PCLIPMSF: 5′-CCC CAA TTG GTC GAC CAT CAT CAA TAATAT ACC TTA TTT TGG-3′ (SEQ ID NO:6) and pCLIPBSRGI: 5′-GCG AAA ATT GTCACT TCC TGT G-3′ (SEQ ID NO:7)). The amplified fragment was digestedwith MunI and BsrGI and cloned into pAd5/Clip (described inInternational Patent Application WO99/55132), which was partiallydigested with EcoRI and after purification digested with BsrGI, therebyre-inserting the left ITR and packaging signal. After restriction enzymeanalysis, the construct was digested with ScaI and SgrAI and an 800 bpfragment was isolated from gel and ligated into ScaI/SgrAI digestedpADAPT+ExSalPac linker. The resulting construct, designatedpIPspSalAdapt, was digested with SalI, dephosphorylated, and ligated tothe phosphorylated ExSalPacF/ExSalPacR double-stranded linker previouslymentioned. A clone in which the PacI site was closest to the ITR wasidentified by restriction analysis and sequences were confirmed bysequence analysis. This novel pAdApt construct, termed pIPspAdapt, thusharbours two ExSalPac linkers containing recognition sequences for PacI,PI-PspI and BstBI, which surround the adenoviral part of the adenoviraladapter construct, and which can be used to linearize the plasmid DNAprior to co-transfection with adenoviral helper fragments.

In order to further increase transgene cloning permutations, a number ofpolylinker variants were constructed based on pIPspAdapt. For thispurpose, pIPspAdapt was first digested with EcoRI and dephosphorylated.A linker composed of the following two phosphorylated and annealedoligos: Ecolinker+: 5′-AAT TCG GCG CGC CGT CGA CGA TAT CGA TAG CGG CCGC-3′ (SEQ ID NO:8) and Ecolinker: 5′-AAT TGC GGC CGC TAT CGA TAT CGT CGACGG CGC GCC G-3′ (SEQ ID NO:9) was ligated into this construct, therebycreating restriction sites for AscI, SalI, EcoRV, ClaI and NotI. Bothorientations of this linker were obtained, and sequences were confirmedby restriction analysis and sequence analysis. The plasmid containingthe polylinker in the order 5′ HindIII, KpnI, Agel, EcoRI, AscI, SalI,EcoRV, ClaI, NotI, NheI, HpaI, BamHI and XbaI was termed pIPspAdapt1,while the plasmid containing the polylinker in the order HindIII, KpnI,Agel, NotI, ClaI, EcoRV, SalI, AscI, EcoRI, NheI, HpaI, BamHI and XbaIwas termed pIPspAdapt2.

To facilitate the cloning of other sense or antisense constructs, alinker composed of the following two oligonucleotides was designed toreverse the polylinker of pIPspAdapt: HindXba+5′-AGC TCT AGA GGA TCC GTTAAC GCT AGC GAA TTC ACC GGT ACC AAG CTT A-3′ (SEQ ID NO:10);HindXba-5′-CTA GTA AGC TTG GTA CCG GTG AAT TCG CTA GCG TTA ACG GAT CCTCTA G-3′ (SEQ ID NO:11). This linker was ligated into HindIII/XbaIdigested pIPspAdapt and the correct construct was isolated. Confirmationwas done by restriction enzyme analysis and sequencing. This newconstruct, pIPspAdaptA, was digested with EcoRI and the previouslymentioned Ecolinker was ligated into this construct. Both orientationsof this linker were obtained, resulting in pIPspAdapt3, which containsthe polylinker in the order XbaI, BamHI, HpaI, NheI, EcoRI, AscI, SalI,EcoRV, ClaI, NotI, Agel, KpnI and HindIII. All sequences were confirmedby restriction enzyme analysis and sequencing.

Adapter plasmids based on Ad35 were then constructed as follows:

The left ITR and packaging sequence corresponding to Ad35 wt sequencesnucleotides 1 to 464 (SEQ ID NO:44) were amplified by PCR on wt Ad35 DNAusing the following primers:

Primer 35F1: (SEQ ID NO:12) 5′-CGG AAT TCT TAA TTA ATC GAC ATC ATC AATAAT ATA CCT TAT AG-3′ Primer 35R2: (SEQ ID NO:13) 5′-GGT GGT CCT AGG CTGACA CCT ACG TAA AAA CAG-3′Amplification introduces a PacI site at the 5′ end and an AvrII site atthe 3′ end of the sequence.

For the amplification, Platinum Pfx DNA polymerase enzyme (LTI) was usedaccording to manufacturer's instructions, but with primers at 0.6 μM andwith DMSO added to a final concentration of 3%. Amplification programwas as follows: 2 min. at 94° C., (30 sec. 94° C., 30 sec. at 56° C., 1min. at 68° C.) for 30 cycles, followed by 10 min. at 68° C.

The PCR product was purified using a PCR purification kit (LTI)according to the manufacturer's instructions and digested with PacI andAvrII. The digested fragment was then purified from gel using theGENECLEAN kit (BIO 101, Inc.). The Ad5-based adapter plasmidpIPspAdApt-3 was digested with AvrII and then partially with PacI andthe 5762 bp fragment was isolated in an LMP agarose gel slice andligated with the above-mentioned PCR fragment digested with the sameenzymes and transformed into electrocompetent DH10B cells (LTI). Theresulting clone is designated pIPspAdApt3-Ad351ITR.

In parallel, a second piece of Ad35 DNA was amplified using thefollowing primers:

35F3: (SEQ ID NO:14) 5′-TGG TGG AGA TCT GGT GAG TAT TGG GAA AAC-3′ 35R4:(SEQ ID NO:15) 5′-CGG AAT TCT TAA TTA AGG GAA ATG CAA ATC TGT GAG G-3′

The sequence of this fragment corresponds to nucleotides 3401 to 4669 ofwt Ad35 (SEQ ID NO:44) and contains 1.3 kb of sequences startingdirectly 3′ from the E1B-55k coding sequence. Amplification andpurification were done as previously described herein for the fragmentcontaining the left ITR and packaging sequence. The PCR fragment wasthen digested with PacI and subcloned into pNEB193 vector (New EnglandBiolabs) digested with SmaI and PacI. The integrity of the sequence ofthe resulting clone was checked by sequence analysis. pNEB/Ad35 pF3R4was then digested with BglII and PacI and the Ad35 insert was isolatedfrom gel using the QIAExII kit (Qiagen). pIPspAdApt3-Ad351ITR wasdigested with BglII and then partially with PacI. The 3624 bp fragment(containing vector sequences, the Ad35 ITR and packaging sequences aswell as the CMV promoter, multiple cloning region and polyA signal) wasalso isolated using the QIAExII kit (Qiagen). Both fragments wereligated and transformed into competent DH10B cells (LTI). The resultingclone, pAdApt35IP3, has the expression cassette from pIPspAdApt3 butcontains the Ad35 left ITR and packaging sequences and a second fragmentcorresponding to nucleotides 3401 to 4669 from Ad35. A second version ofthe Ad35 adapter plasmid having the multiple cloning site in theopposite orientation was made as follows:

pIPspAdapt1 was digested with NdeI and BglII and the 0.7 kbp bandcontaining part of the CMV promoter, the MCS and SV40 polyA was isolatedand inserted in the corresponding sites of pAdApt35IP3 generatingpAdApt35IP1 (FIG. 5).

pAdApt35.LacZ and pAdApt35.Luc adapter plasmids were then generated byinserting the transgenes from pcDNA.LacZ (digested with KpnI and BamHI)and pAdApt.Luc (digested with HindIII and BamHI) into the correspondingsites in pAdApt35IP1. The generation of pcDNA.LacZ and pAdApt.Luc isdescribed in International Patent Publication WO99/55132.

2) Construction of Cosmid pWE.Ad35.pIX-rITR

FIG. 6 presents the various steps undertaken to construct the cosmidclone containing Ad35 sequences from bp 3401 to 34794 (end of the rightITR) that are described in detail below.

2) Construction of Cosmid pWE.Ad35.pIX-rITR

A first PCR fragment (pIX-NdeI) was generated using the following primerset:

35F5: (SEQ ID NO:16) 5′-CGG AAT TCG GGG GGG GGG TGA GTA TTG GGA AAA C-3′35R6: (SEQ ID NO:17) 5′-GGG GAG ATC GTC TAG AGA AGA G-3′

DNA polymerase Pwo (Roche) was used according to manufacturer'sinstructions, however, with an end concentration of 0.6 μM of bothprimers and using 50 ngr wt Ad35 DNA as template. Amplification was doneas follows: 2 min. at 94° C., 30 cycles of 30 sec. at 94° C., 30 sec. at65° C. and 1 min. 45 sec. at 72° C., followed by 8 min. at 68° C. Toenable cloning in the TA cloning vector PCR2.1, a last incubation with 1unit superTaq polymerase (HT Biotechnology LTD) for 10 min. at 72° C.was performed.

The 3370 bp amplified fragment contains Ad35 sequences from bp 3401 to6772 with a NotI site added to the 5′ end. Fragments were purified usingthe PCR purification kit (LTI).

A second PCR fragment (NdeI-rITR) was generated using the followingprimers:

35F7: (SEQ ID NO:18) 5′-GAA TGC TGG CTT CAG TTG TAA TC-3′ 35R8: (SEQ IDNO:19) 5′-CGG AAT TCG CGG CCG CAT TTA AAT CAT CAT CAA TAA TAT ACC-3′

Amplification was done with pfx DNA polymerase (LTI) according tomanufacturer's instructions but with 0.6 μM of both primers and 3% DMSOusing 10 ngr. of wt Ad35 DNA as template. The program was as follows: 3min. at 94° C. and 5 cycles of 30 sec. at 94° C., 45 sec. at 40° C., 2min. 45 sec. at 68° C. followed by 25 cycles of 30 sec. at 94° C., 30sec. at 60° C., 2 min. 45 sec. at 68° C. To enable cloning in theTA-cloning vector PCR2.1, a last incubation with 1 unit superTaqpolymerase for 10 min. at 72° C. was performed. The 1.6 kb amplifiedfragment ranging from nucleotides 33178 to the end of the right ITR ofAd35, was purified using the PCR purification kit (LTI).

Both purified PCR fragments were ligated into the PCR2.1 vector of theTA-cloning kit (Invitrogen) and transformed into STBL-2 competent cells(LTI). Clones containing the expected insert were sequenced to confirmcorrect amplification. Next, both fragments were excised from the vectorby digestion with NotI and NdeI and purified from gel using theGENECLEAN kit (BIO 101, Inc.). Cosmid vector pWE15 (Clontech) wasdigested with NotI, dephosphorylated and also purified from gel. Thesethree fragments were ligated and transformed into STBL2 competent cells(LTI). One of the correct clones that contained both PCR fragments wasthen digested with NdeI, and the linear fragment was purified from gelusing the GENECLEAN kit. Ad35 wt DNA was digested with NdeI and the 26.6kb fragment was purified from LMP gel using agarase enzyme (Roche)according to the manufacturer's instructions. These fragments wereligated together and packaged using λ1 phage packaging extracts(Stratagene) according to the manufacturer's protocol. After infectioninto STBL-2 cells, colonies were grown on plates and analyzed forpresence of the complete insert. One clone with the large fragmentinserted in the correct orientation and having the correct restrictionpatterns after independent digestions with three enzymes (NcoI, PvuIIand ScaI) was selected. This clone is designated pWE.Ad35.pIX-rITR. Itcontains the Ad35 sequences from bp 3401 to the end and is flanked byNotI sites (FIG. 7).

3) Generation of Ad35-based recombinant viruses on PER.C6

Wild type Ad35 virus can be grown on PER.C6 packaging cells to very hightiters. However, whether the Ad5-E1 region that is present in PER.C6 isable to complement E1-deleted Ad35 recombinant viruses is unknown. Totest this, PER.C6 cells were cotransfected with the above-describedadapter plasmid pAdApt35.LacZ and the large backbone fragmentpWE.Ad35.pIX-rITR. First, pAdApt35.LacZ was digested with PacI andpWE.Ad35.pIX-rITR was digested with NotI. Without further purification,4 μgr of each construct was mixed with DMEM (LTI) and transfected intoPER.C6 cells, seeded at a density of 5×10⁶ cells in a T25 flask the daybefore, using Lipofectamin (LTI) according to the manufacturer'sinstructions. As a positive control, 6 μgr of PacI digestedpWE.Ad35.pIX-rITR DNA was cotransfected with a 6.7 kb NheI fragmentisolated from Ad35 wt DNA containing the left end of the viral genomeincluding the E1 region. The next day, medium (DMEM with 10% FBS and 10mM MgCl₂) was refreshed and cells were further incubated. At day 2following the transfection, cells were trypsinized and transferred toT80 flasks. The positive control flask showed CPE at five days followingtransfection, showing that the pWE.Ad35.pIX-rITR construct isfunctional, at least in the presence of Ad35-E1 proteins. Thetransfection with the Ad35 LacZ adapter plasmid and pWE.Ad35.pIX-rITRdid not give rise to CPE. These cells were harvested in the medium atday 10 and freeze/thawed once to release virus from the cells. 4 ml ofthe harvested material was added to a T80 flask with PER.C6 cells (at80% confluency) and incubated for another five days. Thisharvest/re-infection was repeated two times but there was no evidencefor virus associated CPE.

From this experiment, it seems that the Ad5-E1 proteins are not, or notwell enough, capable of complementing Ad35 recombinant viruses. However,it may be that the sequence overlap of the adapter plasmid and thepWE.Ad35.pIX-rITR backbone plasmid is not large enough to efficientlyrecombine and give rise to a recombinant virus genome. The positivecontrol transfection was done with a 6.7 kb left end fragment and,therefore, the sequence overlap was about 3.5 kb. The adapter plasmidand the pWE.Ad35.pIX-rITR fragment have a sequence overlap of 1.3 kb. Tocheck whether the sequence overlap of 1.3 kb is too small for efficienthomologous recombination, a co-transfection was done with PacI digestedpWE.Ad35.pIX-rITR and a PCR fragment of Ad35 wt DNA generated with theabove-mentioned 35F1 and 35R4 using the same procedures as previouslydescribed herein. The PCR fragment thus contains left end sequences upto bp 4669 and, therefore, has the same overlap sequences withpWE.Ad35.pIX-rITR as the adapter plasmid pAdApt35.LacZ, but has Ad35-E1sequences. Following PCR column purification, the DNA was digested withSalI to remove possible intact template sequences. A transfection withthe digested PCR product alone served as a negative control. Four daysafter the transfection, CPE occurred in the cells transfected with thePCR product and the Ad35 pIX-rITR fragment, and not in the negativecontrol. This result shows that a 1.3 kb overlapping sequence issufficient to generate viruses in the presence of Ad35-E1 proteins. Fromthese experiments, we conclude that the presence of at least one of theAd35-E1 proteins is necessary to generate recombinant Ad35 based vectorsfrom plasmid DNA on Ad5 complementing cell lines.

Example 5

1) Construction of Ad35-E1 Expression Plasmids

Since Ad5-E1 proteins in PER.C6 are incapable of complementing Ad35recombinant viruses efficiently, Ad35-E1 proteins have to be expressedin Ad5 complementing cells (e.g., PER.C6). Alternatively, a newpackaging cell line expressing Ad35-E1 proteins has to be made, startingfrom either diploid primary human cells or established cell lines notexpressing adenovirus E1 proteins. To address the first possibility, theAd35-E1 region was cloned in expression plasmids as described below.

First, the Ad35-E1 region from bp 468 to bp 3400 was amplified from wtAd35 DNA using the following primer set:

35F11: (SEQ ID NO:20) 5′-GGG GTA CCG AAT TCT CGC TAG GGT ATT TAT ACC-3′35F10: (SEQ ID NO:21) 5′-GGT CTA GAC CTG CAG GTT AGT CAG TTT CTT CTC CACTG-3′

This PCR introduces a KpnI and EcoRI site at the 5′ end and an SbfI andXbaI site at the 3′ end.

Amplification on 5 ngr. template DNA was done with Pwo DNA polymerase(Roche) using the manufacturer's instructions, however, with bothprimers at a final concentration of 0.6 μM. The program was as follows:2 min. at 94° C., 5 cycles of 30 sec. at 94° C., 30 sec. at 56° C. and 2min. at 72° C., followed by 25 cycles of 30 sec. at 94° C., 30 sec. at60° C. and 2 min. at 72° C., followed by 10 min. at 72° C. PCR productwas purified by a PCR purification kit (LTI) and digested with KpnI andXbaI. The digested PCR fragment was then ligated to the expressionvector pRSVhbvNeo (see below) also digested with KpnI and XbaI.Ligations were transformed into competent STBL-2 cells (LTI) accordingto manufacturer's instructions and colonies were analyzed for thecorrect insertion of Ad35-E1 sequences into the polylinker in betweenthe RSV promoter and HBV polyA.

The resulting clone was designated pRSV.Ad35-E1 (FIG. 8). The Ad35sequences in pRSV.Ad35-E1 were checked by sequence analysis.

pRSVhbvNeo was generated as follows: pRc-RSV (Invitrogen) was digestedwith PvuII, dephosphorylated with TSAP enzyme (LTI), and the 3 kb vectorfragment was isolated in low melting point agarose (LMP). PlasmidpPGKneopA (FIG. 9; described in International Patent ApplicationWO96/35798) was digested with SspI completely to linearize the plasmidand facilitate partial digestion with PvuII. Following the partialdigestion with PvuII, the resulting fragments were separated on a LMPagarose gel and the 2245 bp PvuII fragment, containing the PGK promoter,neomycin-resistance gene and HBVpolyA, was isolated. Both isolatedfragments were ligated to give the expression vector pRSV-pNeo that nowhas the original SV40prom-neo-SV40polyA expression cassette replaced bya PGKprom-neo-HBVpolyA cassette (FIG. 10). This plasmid was furthermodified to replace the BGHpA with the HBVpA as follows: pRSVpNeo waslinearized with ScaI and further digested with XbaI. The 1145 bpfragment, containing part of the Amp gene and the RSV promoter sequencesand polylinker sequence, was isolated from gel using the GENECLEAN kit(Bio Inc. 101). Next, pRSVpNeo was linearized with ScaI and furtherdigested partially with EcoRI and the 3704 bp fragment containing thePGKneo cassette and the vector sequences were isolated from gel asabove. A third fragment, containing the HBV polyA sequence flanked byXbaI and EcoRI at the 5′ and 3′ end, respectively, was then generated byPCR amplification on pRSVpNeo using the following primer set:

(SEQ ID NO:22) HBV-F: 5′-GGC TCT AGA GAT CCT TCG CGG GAC GTC-3′ and (SEQID NO:23) HBV-R: 5′-GGC GAA TTC ACT GCC TTC CAC CAA GC-3′.

Amplification was done with Elongase enzyme (LTI) according to themanufacturer's instructions with the following conditions: 30 seconds at94° C., then 5 cycles of 45 seconds at 94° C., 1 minute at 42° C. and 1minute at 68° C., followed by 30 cycles of 45 seconds at 94° C., 1minute at 65° C. and 1 minute at 68° C., followed by 10 minutes at 68°C. The 625 bp PCR fragment was then purified using the Qiaquick PCRpurification kit, digested with EcoRI and XbaI and purified from gelusing the GENECLEAN kit. The three isolated fragments were ligated andtransformed into DH5α competent cells (LTI) to give the constructpRSVhbvNeo (FIG. 11). In this construct, the transcription regulatoryregions of the RSV expression cassette and the neomycin selection markerare modified to reduce overlap with adenoviral vectors that oftencontain CMV and SV40 transcription regulatory sequences.

2) Generation of Ad35 Recombinant Viruses on PER.C6 Cells Cotransfectedwith an Ad35-E1 Expression Construct.

PER.C6 cells were seeded at a density of 5×10⁶ cells in a T25 flask and,the next day, transfected with a DNA mixture containing:

-   1 μg pAdApt35.LacZ digested with PacI-   5 μgpRSV.Ad35E1 undigested-   2 μg pWE.Ad35.pIX-rITR digested with NotI

Transfection was done using Lipofectamine according to themanufacturer's instructions. Five hours after addition of thetransfection mixture to the cells, medium was removed and replaced byfresh medium. After two days, cells were transferred to T80 flasks andfurther cultured. One week post-transfection, 1 ml of the medium wasadded to A549 cells and, the following day, cells were stained for LacZexpression. Blue cells were clearly visible after two hours of stainingindicating that recombinant LacZ expressing viruses were produced. Thecells were further cultured, but no clear appearance of CPE was noted.However, after 12 days, clumps of cells appeared in the monolayer and 18days following transfection, cells were detached. Cells and medium werethen harvested, freeze-thawed once, and 1 ml of the crude lysate wasused to infect PER.C6 cells in a 6-well plate. Two days after infection,cells were stained for LacZ activity. After two hours, 15% of the cellswere stained blue. To test for the presence of wt and/or replicatingcompetent viruses, A549 cells were infected with these viruses andfurther cultured. No signs of CPE were found indicating the absence ofreplication-competent viruses. These experiments show that recombinantAdApt35.LacZ viruses were made on PER.C6 cells cotransfected with anAd35-E1 expression construct.

Ad35 recombinant viruses escape neutralization in human serum containingneutralizing activity to Ad5 viruses.

The AdApt35.LacZ viruses were then used to investigate infection in thepresence of serum that contains neutralizing activity to Ad5 viruses.Purified Ad5-based LacZ virus served as a positive control for NA.Hereto, PER.C6 cells were seeded in a 24-well plate at a density of2×10⁵ cells/well. The next day, a human serum sample with highneutralizing activity to Ad5 was diluted in culture medium in five stepsof five times dilutions. 0.5 ml of diluted serum was then mixed with4×10⁶ virus particles AdAptS.LacZ virus in 0.5 ml medium and after 30minutes of incubation at 37° C., 0.5 ml of the mixture was added toPER.C6 cells in duplicate. For the AdApt35.LacZ viruses, 0.5 ml of thediluted serum samples were mixed with 0.5 ml crude lysate containingAdApt35.LacZ virus and, after incubation, 0.5 ml of this mixture wasadded to PER.C6 cells in duplo. Virus samples incubated in mediumwithout serum were used as positive controls for infection. After twohours of infection at 37° C., medium was added to reach a final volumeof 1 ml and cells were further incubated. Two days after infection,cells were stained for LacZ activity. The results are shown in Table II.From these results, it is clear that whereas AdApt5.LacZ viruses areefficiently neutralized, AdApt35.LacZ viruses remain infectiousirrespective of the presence of human serum. This proves thatrecombinant Ad35-based viruses escape neutralization in human sera thatcontain NA to Ad5-based viruses.

Example 6

Generation of Cell Lines Capable of Complementing E1-Deleted Ad35Viruses

Generation of pIG135 and pIG270

Construct pIG.E1A.E1B (FIG. 12) contains E1 region sequences of Ad5corresponding to nucleotides 459 to 3510 of the wt Ad5 sequence (Genbankaccession number M72360) operatively linked to the humanphosphoglycerate kinase promoter (“PGK”) and the Hepatitis B Virus polyAsequences. The generation of this construct is described inInternational Patent Application No. WO97/00326. The E1 sequences of Ad5were replaced by corresponding sequences of Ad35 as follows.pRSV.Ad35-E1 (described in Example 5) was digested with EcoRI andSse83871 and the 3 kb fragment corresponding to the Ad35-E1 sequenceswas isolated from gel. Construct pIG.E1A.E1B was digested with Sse83871completely and partially with EcoRI. The 4.2 kb fragment correspondingto vector sequences without the Ad5-E1 region but retaining the PGKpromoter were separated from other fragments on LMP agarose gel and thecorrect band was excised from gel. Both obtained fragments were ligatedresulting in pIG.Ad35-E1.

This vector was further modified to remove the LacZ sequences present inthe pUCI 19 vector backbone. Hereto, the vector was digested with BsaAIand BstXI and the large fragment was isolated from gel. A doublestranded oligo was prepared by annealing the following two oligos:

BB1: 5′-GTG CCT AGG CCA CGG GG-3′ (SEQ ID NO:24) and BB2: 5′-GTG GCC TAGGCA C-3′. (SEQ ID NO:25)

Ligation of the oligo and the vector fragment resulted in constructpIG135 (FIG. 13). Correct insertion of the oligo restores the BsaAI andBstXI sites and introduces a unique AvrII site. Next, we introduced aunique site at the 3′end of the Ad35-E1 expression cassette in pIG135.Hereto, the construct was digested with SapI and the 3′ protruding endswere made blunt by treatment with T4 DNA polymerase. The thus treatedlinear plasmid was further digested with BsrGI and the largevector-containing fragment was isolated from gel. To restore the 3′ endof the HBVpolyA sequence and to introduce a unique site, a PCR fragmentwas generated using the following primers:

(SEQ ID NO:26) 270F: 5′-CAC CTC TGC CTA ATC ATC TC-3′ and (SEQ ID NO:27)270R: 5′-GCT CTA GAA ATT CCA CTG CCT TCC ACC-3′.

The PCR was performed on pIG.Ad35.E1 DNA using Pwo polymerase (Roche)according to the manufacturer's instructions. The obtained PCR productwas digested with BsrGI and dephosphorylated using Tsap enzyme (LTI),the latter to prevent insert dimerization on the BsrGI site. The PCRfragment and the vector fragment were ligated to yield construct pIG270(FIG. 14).

Ad35-E1 Sequences are Capable of Transforming Rat Primary Cells

Newborn WAG/RIJ rats were sacrificed at 1 week of gestation and kidneyswere isolated. After careful removal of the capsule, kidneys weredisintegrated into a single cell suspension by multiple rounds ofincubation in trypsin/EDTA (LTI) at 37° C. and collection of floatingcells in cold PBS containing 1% FBS. When most of the kidney wastrypsinized, all cells were re-suspended in DMEM supplemented with 10%FBS and filtered through a sterile cheesecloth. Baby Rat Kidney (BRK)cells obtained from one kidney were plated in 5 dishes (Greiner, 6 cm).When a confluency of 70-80% was reached, the cells were transfected with1 or 5 μgr DNA/dish using the CaPO₄ precipitation kit (LTI) according tothe manufacturer's instructions. The following constructs were used inseparate transfections: pIG.E1A.E1B (expressing the Ad5-E1 region),pRSV.Ad35-E1, pIG.Ad35-E1 and pIG270 (expressing the Ad35-E1 region).Cells were incubated at 37° C., 5% CO₂ until foci of transformed cellsappeared. Table III shows the number of foci that resulted from severaltransfection experiments using circular or linear DNA. As expected, theAd5-E1 region efficiently transformed BRK cells. Foci also appeared inthe Ad35-E1 transfected cell layer although with lower efficiency. TheAd35 transformed foci appeared at a later time point: ˜2 weeks posttransfection compared with 7-10 days for Ad5-E1. These experimentsclearly show that the E1 genes of the B group virus Ad35 are capable oftransforming primary rodent cells. This proves the functionality of theAd35-E1 expression constructs and confirms earlier findings of thetransforming capacity of the B-group viruses Ad3 and Ad7 (Dijkema,1979). To test whether the cells in the foci were really transformed, afew foci were picked and expanded. From the 7 picked foci, at least 5turned out to grow as established cell lines.

Generation of New Packaging Cells Derived from Primary Human Amniocytes

Amniotic fluid obtained after amniocentesis was centrifuged and cellswere re-suspended in AmnioMax medium (LTI) and cultured in tissueculture flasks at 37° C. and 10% CO₂. When cells were growing nicely(approximately one cell division/24 hrs.), the medium was replaced witha 1:1 mixture of AmnioMax complete medium and DMEM low glucose medium(LTI) supplemented with Glutamax I (end concentration 4 mM, LTI) andglucose (end concentration 4.5 gr/L, LTI) and 10% FBS (LTI). Fortransfection ˜5×10⁵ cells were plated in 10 cm tissue culture dishes.The day after, cells were transfected with 20 μgr of circularpIG270/dish using the CaPO₄ transfection kit (LTI) according tomanufacturer's instructions and cells were incubated overnight with theDNA precipitate. The following day, cells were washed 4 times with PBSto remove the precipitate and further incubated for over three weeksuntil foci of transformed cells appeared. Once a week the medium wasreplaced by fresh medium. Other transfection agents like, but notlimited to, LipofectAmine (LTI) or PEI (Polyethylenimine, high molecularweight, water-free, Aldrich) were used. Of these three agents, PEIreached the best transfection efficiency on primary human amniocytes:˜1% blue cells 48 hrs.

Following Transfection of pAdApt35.LacZ

Foci are isolated as follows. The medium is removed and replaced by PBSafter which foci are isolated by gently scraping the cells using a50-200 μl Gilson pipette with a disposable filter tip. Cells containedin ˜10 μml PBS were brought in a 96-well plate containing 15 μltrypsin/EDTA (LTI) and a single cell suspension was obtained bypipetting up and down and a short incubation at room temperature. Afteraddition of 200 μl of the above described 1:1 mixture of AmnioMaxcomplete medium and DMEM with supplements and 10% FBS, cells werefurther incubated. Clones that continued to grow were expanded andanalyzed for their ability to complement growth of E1-deleted adenoviralvectors of different sub-groups, specifically ones derived from B-groupviruses, and more specifically from Ad35 or Ad11.

Generation of New Packaging Cell Lines from HER Cells

HER cells are isolated and cultured in DMEM medium supplemented with 10%FBS (LTI). The day before transfection, ˜5×10⁵ cells are plated in 6 cmdishes and cultured overnight at 37° C. and 10% CO₂. Transfection isdone using the CaPO₄ precipitation kit (LTI) according to themanufacturer's instructions. Each dish is transfected with 8-10 μmgrpIG270 DNA, either as a circular plasmid or as a purified fragment. Toobtain the purified fragment, pIG270 was digested with AvrII and XbaIand the 4 kb fragment corresponding to the Ad35-E1 expression cassettewas isolated from gel by agarase treatment (Roche). The following day,the precipitate is washed away carefully by four washes with sterilePBS. Then fresh medium is added and transfected cells are furthercultured until foci of transformed cells appear. When large enough (>100cells), foci are picked and brought into 96-wells as described above.Clones of transformed HER cells that continue to grow, are expanded andtested for their ability to complement growth of E1-deleted adenoviralvectors of different sub-groups, specifically ones derived from B-groupviruses, and more specifically from Ad35 or Ad11.

New Packaging Cell Lines Derived from PER.C6

As described in Example 5, it is possible to generate and growAd35-E1-deleted viruses on PER.C6 cells with cotransfection of anAd35-E1 expression construct, e.g., pRSV.Ad35.E1. However, large-scaleproduction of recombinant adenoviruses using this method is cumbersomebecause, for each amplification step, a transfection of the Ad35-E1construct is needed. In addition, this method increases the risk ofnon-homologous recombination between the plasmid and the virus genomewith high chances of generation of recombinant viruses that incorporateE1 sequences resulting in replication-competent viruses. To avoid this,the expression of Ad35-E1 proteins in PER.C6 has to be mediated byintegrated copies of the expression plasmid in the genome. Since PER.C6cells are already transformed and express Ad5-E1 proteins, addition ofextra Ad35-E1 expression may be toxic for the cells. However, it is notimpossible to stably transfect transformed cells with E1 proteins sinceAd5-E1-expressing A549 cells have been generated.

In an attempt to generate recombinant adenoviruses derived from subgroupB virus Ad7, Abrahamsen et al. (1997) were not able to generateE1-deleted viruses on 293 cells without contamination of wt Ad7. Virusesthat were picked after plaque purification on 293-ORF6 cells (Brough etal., 1996) were shown to have incorporated Ad7-E1B sequences bynonhomologous recombination. Thus, efficient propagation of Ad7recombinant viruses proved possible only in the presence of Ad7-E1Bexpression and Ad5-E4-ORF6 expression. The E1B proteins are known tointeract with cellular as well as viral proteins (Bridge et al., 1993;White, 1995). Possibly, the complex formed between the E1B-55K proteinand E4-ORF6 which is necessary to increase mRNA export of viral proteinsand to inhibit export of most cellular mRNAs is critical and, in someway, serotype-specific. The above experiments suggest that the E1Aproteins of Ad5 are capable of complementing an Ad7-E1A deletion andthat Ad7-E1B expression in adenovirus packaging cells on itself is notenough to generate a stable complementing cell line. To test whether oneor both of the Ad35-E1B proteins is/are the limiting factor in efficientAd35 vector propagation on PER.C6 cells, we have generated an Ad35adapter plasmid that does contain the E1B promoter and E1B sequences butlacks the promoter and the coding region for E1A. Hereto, the left endof wt Ad35 DNA was amplified using the primers 35F1 and 35R4 (bothdescribed in Example 4) with Pwo DNA polymerase (Roche) according to themanufacturer's instructions. The 4.6 kb PCR product was purified usingthe PCR purification kit (LTI) and digested with SnaBI and ApaI enzymes.The resulting 4.2 kb fragment was then purified from gel using theQIAEXII kit (Qiagen). Next, pAdApt35IP1 (Example 4) was digested withSnaBI and ApaI and the 2.6 kb vector-containing fragment was isolatedfrom gel using the GENECLEAN kit (BIO 101, Inc). Both isolated fragmentswere ligated to give pBr/Ad35.leftITR-pIX (FIG. 15). Correctamplification during PCR was verified by a functionality test asfollows: The DNA was digested with BstBI to liberate the Ad35 insertfrom vector sequences and 4 μg of this DNA was cotransfected with 4 μgof NotI digested pWE/Ad35.pIX-rITR (Example 4) into PER.C6 cells. Thetransfected cells were passaged to T80 flasks at day 2 and again twodays later CPE had formed showing that the new pBr/Ad35.leftITR-pIXconstruct contains functional E1 sequences. The pBr/Ad35.leftITR-pIXconstruct was then further modified as follows. The DNA was digestedwith SnaBI and HindIII and the 5′ HindIII overhang was filled in usingKlenow enzyme. Religation of the digested DNA and transformation intocompetent cells (LTI) gave construct pBr/Ad35.leftITR-pIXΔDE1A (FIG.16). This latter construct contains the left end 4.6 kb of Ad35 exceptfor EIA sequences between bp 450 and 1341 (numbering according to SEQ IDNO:44) and thus lacks the E1A promoter and most of the E1A codingsequences. pBr/Ad35.leftITR-pIXΔDE1A was then digested with BstBI and 2μg of this construct was cotransfected with 6 μmgr of NotI digestedpWE/Ad35.pIX-rITR (Example 4) into PER.C6 cells. One week followingtransfection, full CPE had formed in the transfected flasks.

This experiment shows that the Ad35-E1A proteins are functionallycomplemented by Ad5-E1A expression in PER.C6 cells and that at least oneof the Ad35-E1B proteins cannot be complemented by Ad5-E1 expression inPER.C6. It further shows that it is possible to make a complementingcell line for Ad35-E1-deleted viruses by expressing Ad35-E1B proteins inPER.C6. Stable expression of Ad35-E1B sequences from integrated copiesin the genome of PER.C6 cells may be driven by the E1B promoter andterminated by a heterologous poly-adenylation signal like, but notlimited to, the HBVpA. The heterologous pA signal is necessary to avoidoverlap between the E1B insert and the recombinant vector, since thenatural E1B termination is located in the pIX transcription unit thathas to be present on the adenoviral vector. Alternatively, the E1Bsequences may be driven by a heterologous promoter like, but not limitedto, the human PGK promoter or by an inducible promoter like, but notlimited to, the 7xtetO promoter (Gossen and Bujard, 1992). Also, inthese cases, the transcription termination is mediated by a heterologouspA sequence, e.g., the HBV pA. The Ad35-E1B sequences at least compriseone of the coding regions of the E1B-21K and the E1B-55K proteinslocated between nucleotides 1611 and 3400 of the wt Ad35 sequence. Theinsert may also include part of the Ad35-E1B sequences betweennucleotides 1550 and 1611 of the wt Ad35 sequence (SEQ ID NO:44).

Example 7

Ad35-Based Viruses Deleted for E1A and E1B-21K Genes EfficientlyPropagate on Ad5 Complementing Cell Lines

The generation of Ad35-based viruses that are deleted for E1A and retainthe full E1B region is described in Example 6 of this application. Suchviruses can be generated and propagated on the Ad5 complementing cellline PER.C6. The E1B region comprises partially overlapping codingsequences for the two major proteins 21K and 55K (Bos et al., 1981).Whereas, during productive wt adenoviral infection, both 21K and 55K areinvolved in counteracting the apoptose-inducing effects of E1A proteins,the E1B-55K protein has been suggested to have additional functionsduring the late phase of virus infection. These include the accumulationof viral mRNAs, the control of late viral gene expression and theshutoff of most host mRNAs at the level of mRNA transport (Babiss etal., 1984, 1985; Pilder et al., 1986). A complex formed between E1B-55Kand the ORF6 protein encoded by the adenovirus early region 4 (Leppardand Shenk, 1989; Bridge and Ketner, 1990) exerts at least part of thesefunctions.

To analyze which of the E1B proteins is required for propagation ofAd35-E1A-deleted recombinant viruses on PER.C6 packaging cells, the E1Bregion in construct pBr.Ad35.leftITR-pIXΔE1A (see Example 6 and FIG. 16)was further deleted. A first construct, pBr.Ad35Δ21K, retains the fullE1B-55K sequence and is deleted for E1A and E1B-21K. Hereto,pBr.Ad35.leftITR-pIXΔE1A was digested with NcoI and BspE1 and the 5 KBvector fragment was isolated from agarose gel using the GENECLEAN kit(BIO 101, Inc.) according to the manufacturer's instructions. Then a PCRfragment was generated with pBr.Ad35.leftITR-pIXΔE1A as template DNAusing the following primers:

(SEQ ID NO:28) 35D21: 5′-TTA GAT CCA TGG ATC CCG CAG ACT C-3′ and (SEQID NO:29) 35B3: 5′-CCT GAG CCC CAT TTC CAG-3′.Amplification was done using Pwo DNA polymerase (Roche) according tomanufacturer's recommendations with the addition of DMSO (finalconcentration 3%) in the reaction mixture. The PCR program was asfollows: 94° C. for 2′, then 30 cycles of 94° C. for 30″, 58° C. for 30″and 72° C. for 45″ and a final step at 68° C. for 8′ to ensure bluntends.

This PCR amplifies Ad35-E1B sequences from nucl. 1908 to 2528 (sequenceAd35, SEQ ID NO:44) and introduces an NcoI site at the start codon ofthe E1B-55K coding sequence (bold in primer 35D21). The 620 bp PCRfragment was purified using the PCR purification kit (Qiagen) and thendigested with NcoI and BspEI, purified from agarose gel as above andligated to the above-described NcoI/BspE1 digested vector fragment togive pBr.Ad35Δ21K (FIG. 17).

Since the coding regions of the 21K and 55K proteins overlap, it is onlypossible to delete part of the 55K coding sequences while retaining 21K.Hereto, pBr.Ad35.leftITR-pIXΔE1A was digested with BglII and the vectorfragment was religated to give pBr.Ad35A55K1 (FIG. 18). This deletionremoves E1B coding sequences from nucl. 2261 to 3330 (Ad35 sequence inSEQ ID NO:44). In this construct the N-terminal 115 amino acids areretained and become fused to 21 additional amino acids out of the properreading frame before a stop codon is encountered. The 21K coding regionis intact in construct pBr.Ad35Δ55K1.

A third construct that has a deletion of E1A, 21K and most of the 55Ksequences was generated as follows. pBr.Ad35.leftITR-pIX (FIG. 15) wasdigested with SnaBI and MfeI (isoschizomer of MunI) and the 5′ overhangresulting from the MfeI digestion was filled in using Klenow enzyme. The4.4 kb vector fragment was isolated from gel using the GENECLEAN kit(BIO 101, Inc.) according to the manufacturer's instructions andreligated to give construct pBr.Ad35ΔSM (FIG. 19). In this construct,the Ad35 sequences between nucl. 453 and 2804 are deleted. Thus, 596nucl. of the 3′ end of E1b-55K are retained. A further deletion of 55Ksequences was made in construct pBr.Ad35ΔE1A.ΔE1B by digestion ofpBr.Ad35.leftITR-pIX with SnaBI and BglII, Klenow treatment to fill inthe BglII cohesive ends, and religation. FIG. 20 shows a schematicrepresentation of the above-mentioned constructs.

To test whether Ad35-based viruses can be generated with theseconstructs, each of the constructs was cotransfected with NotI digestedpWE.Ad35pIX-rITR (see, Example 4) onto PER.C6 cells. Hereto, therespective fragments were PCR amplified using primers 35F1 and 35R4(see, Example 4). This PCR amplification was done since some of theconstructs were difficult to isolate in large enough quantities. In thisway, equal quality of the different adapter fragments was ensured. Forthe amplification, Pwo DNA polymerase (Roche) was used according to themanufacturer's instructions but with DMSO (3% final concentration) addedto the PCR mixture. Of each template ˜50 ng DNA was used. The conditionsfor the PCR were as follows: 94° C. for 2′, then 5 cycles of 94° C. for30″, 48° C. for 45″ and 72° C. for 4′ followed by 25 cycles of 94° C.for 30″, 60° C. for 30″ and 72° C. for 4′ and a final step at 68° C. for8′.

PCR fragments were generated from pBr.Ad35.leftITR-pIX,pBr.Ad35.leftITR-pIXΔE1A, pBr.Ad35Δ21K, pBr.Ad35Δ55K1, pBr.Ad35ΔSM andpBr.Ad35ΔE1AΔE1B. All fragments were using the PCR purification kit(Qiagen) according to manufacturer's instructions and finalconcentrations were estimated on EtBr stained agarose gel using theEagle Eye II Still Video system and EagleSight software (Stratagene)with the SmartLadder molecular weight marker (Eurogentec) as reference.

PER.C6 cells were seeded at a density of 2.5×10⁶ cells in a T25culturing flask in DMEM containing 10% fetal calf serum (FCS) and 10 mMMgSO₄ and cultured in a humidified stove at 37° C., 10% CO₂. The nextday, 3 mg of each of the PCR fragments was cotransfected with 5 μgr NotIdigested pWE.Ad35pIX-rITR using LipofectAmine (GIBCO, Life TechnologiesInc.) according to the manufacturer's instructions. Two days after thetransfection, all cells were passed to a T80 flask and further cultured.Cultures were then monitored for the appearance of CPE. In line with theoutcome of previous experiments described in Examples 4 and 6,pBr.Ad35.leftITR-pIX and pBr.Ad35.leftITR-pIXΔE1A showed almost full CPEwithin one week following transfection. Of the fragments with differentE1B deletions, only pBr.Ad35Δ21K showed CPE at the same time as theabove two fragments. Constructs pBr.Ad35Δ55K1, pBr.Ad35ΔSM andpBr.Ad35ΔE1AΔE1B did not give CPE at all, not even after harvesting byfreeze-thawing and re-infection of the crude lysate onto fresh PER.C6cells.

From these experiments, it can be concluded that Ad35-E1B-55K, and notE1B-21K, is necessary for generation and propagation of Ad35-basedviruses on Ad5 complementing cell lines. Therefore, Ad35-based viruseshaving a deletion of the E1A and E1B-21K genes and having the E1B-55Kgene or a functional fragment thereof, can be grown on Ad5 complementingcell lines. Alternatively, Ad35-based viruses can be grown on PER.C6cells that stably express the full E1B region or the E1B-55K gene, or afunctional fragment thereof. The Ad35-E1B-55K gene, or functional partsthereof, may be expressed from a heterologous promoter like, but notlimited to, the human PGK promoter, the human cytomegalovirus immediateearly promoter (CMV), Rous sarcoma virus promoter, etc., and terminatedby a heterologous poly adenylation sequence (PA) like, but not limitedto, the hepatitis B virus poly adenylation sequence (HBVpA) and theSimian Virus 40 poly adenylation sequence (SV40pA), etc. As nonlimitingexamples, PER.C6 cells that express the Ad35-E1B region driven by theE1B promoter and HBVpA, PER.C6 cells that express the Ad35-E1B regiondriven by the human PGK promoter and HBVpA and PER.C6 cells that expressa functional fragment of Ad35-E1B-55K driven by the human PGK promoterand HBVpA are described below.

We describe the generation of two expression constructs, pIG.35BS andpIG.35BL, that both carry the Ad35-E1B genes and a neomycin selectionmarker. The two constructs differ in the length of the fragmentcontaining the E1B promoter. In 35BL, the promoter fragment is longerand includes the 3′ end of the E1A region (103 nucl. coding sequence andpA). The E1B region is terminated by the HBVpolyA and the neo^(r) geneis driven by a hPGK promoter/HBVpA cassette.

pIG.35BL was made as follows. Construct pRSV.Ad35E1 (described inExample 5, FIG. 8) was digested with NruI and HindIII and the protrudingends were filled in by Klenow treatment. The 7 kb vector fragment wasseparated from the smaller fragment on gel and isolated using theGENECLEAN kit (BIO 101, Inc.). After religation of the DNA andtransformation into competent STBL2 cells (Gibco, LTI), correct cloneswere isolated. pIG.35BL (FIG. 21) contains 273 nucl. upstream of thestart site of the E1B-21K coding region.

pIG.35BS was made in the same way as pIG.35BL except that pRSV.Ad35E1was digested with NruI and HpaI (both enzymes leave blunt ends),resulting in a shorter fragment upstream of the coding region ofE1B-21K: 97 nucleotides.

To generate Ad35-E1B expressing cells, PER.C6 cells were seeded in 10 cmdishes at 1×10⁶ cells/dish. Two days later, cells were transfected withScaI linearized constructs. Four dishes were transfected with 1 and fourwith 2 μg DNA (total of 16 dishes; Lipofectamine (Gibco, LTI), nocarrier DNA used) according to the manufacturer's instructions. The nextday, transfected cells received G418-containing medium (0.75 mg/ml).Control transfections using LacZ expression constructs (2 μg) werestained after 48 hrs and showed a transfection efficiency of ˜25%. Fourdays following addition of selection medium, untransfected cells startedto die and again, three days later, clones were becoming visible. A weeklater, the first clones were picked. Transfection with 1 μg resulted inless and also, initially, smaller clones (total ˜20 clones/dishagainst>50 clones/dish for the transfection with 2 μg DNA). The positivecontrol transfection using 2 μg pcDNA3 (Invitrogen) resulted in ˜50clones.

In total, 120 clones were picked and 107 were successfully established(55 from pIG35BS and 52 from pIG35BL).

Generation of pIG35Bneo

pIG35Bneo is an Ad35-E1B expression plasmid from which the E1B genes areexpressed from a heterologous promoter (hPGK) and that also contains aneomycin resistance expression cassette. To avoid instability of theplasmid due to recombination events on homologous sequences, the RSVpromoter drives the neo^(r) gene. To achieve this, construct pRSVhbv.Neo(described in Example 5, FIG. 11) was digested with ScaI and BamHI andprotruding ends were filled in using Klenow enzyme. The 1070 bp fragmentcontaining part of the Ampicilin gene and the RSV promoter was isolatedfrom gel using the GENECLEAN kit (BIO 101, Inc.). Next, pRSVhbvNeo wasdigested with ScaI and EcoRI, blunted with Klenow and the 3.2 kbfragment containing the neo gene, HBVpA, vector and part of theAmpicilin gene was isolated as above. The two fragments were thenligated to give pRSVneo4 (FIG. 22). Construct pIG270 (FIG. 14, describedin Example 6) was then digested with EcoRI and NcoI and sticky ends wereblunted with Klenow enzyme. The vector-containing fragment was isolatedfrom gel as described above and religated to give pIG270delE1A. Thisconstruct was digested with AvrII and XbaI and protruding ends werefilled in using Klenow enzyme. The 2.9 kb fragment containing the HPGKpromoter and Ad35-E1B sequences was isolated from gel as above. Next,pRSVneo4 was digested with BglII, blunted with Klenow enzyme,dephosphorylated and isolated from gel. The blunted AvrII/XbaI Ad35-E1Bfragment was then ligated with the above prepared pRSVneo4 vectorfragment and resulting clones were analyzed. One clone that containedboth expression cassettes in the same orientation was chosen and namedpIG35Bneo (FIG. 23). Detailed analysis of this clone revealed that anextra BglII site was present, probably due to an incomplete Klenowreaction (BglII site at nucl. 2949 in FIG. 23).

Generation of pIG35.55K

Construct pIG35.55K is similar to pIG35Bneo, however, it lacks thecoding region of Ad35-E1B-21K. Hereto, both the E1A and E1B-21Ksequences are first deleted from pIG270 as follows:

Construct pIG270 is digested with EcoRI, treated with Klenow enzyme andpurified using a PCR purification kit (Qiagen) according to themanufacturer's instructions. The recovered DNA is then digested withAgel and the ˜5 kb vector fragment was isolated from gel as above. Next,Ad35-E1B-55K sequences are amplified by PCR on pIG270 template DNA usingthe following primers:

(SEQ ID NO:28) 35D21: 5′-TTA GAT CCA TGG ATC CCG CAG ACT C-3′ and (SEQID NO:29) 35B3: 5′-CCT GAG CCC CAT TTC CAG-3′The conditions used for the amplification are as previously described.The PCR fragment is purified using the PCR purification kit (Qiagen) anddigested with NcoI. Following Klenow treatment to fill in the protrudingends, the DNA is further digested with Agel and again column purified.The thus treated PCR fragment is then cloned into the above preparedEcoRI/Agel digested vector fragment to give pIG270.ΔE1AΔ21K. The laststeps to obtain pIG35.55K (FIG. 24) are equivalent to the last stepsdescribed above for the generation of pIG35Bneo, starting withpIG270.ΔE1AΔ21K instead of pIG270.ΔE1A.

-   -   pIG35.55K is then linearized with ScaI and used to transfect        PER.C6 cells as described above. Clones that are resistant to        G418 selection are picked and analyzed for their ability to        complement the propagation of E1-deleted Ad35 viruses.

Example 8

New Packaging Cell Lines for the Generation and Propagation ofE1-Deleted Ad35-Based Vectors Derived from Primary Human Cells

The complete morphological transformation of primary cells by adenovirusE1 genes is the result of the combined activities of the proteinsencoded by the E1A and E1B regions. The roles of the different E1proteins in lytic infection and in transformation have been studiedextensively (reviewed in Zantema and van der Eb, 1995; White, 1995,1996). The adenovirus E1A proteins are essential for transformation ofprimary cells. The E1A proteins exert this effect through directinteraction with a number of cellular proteins that are involved inregulation of transcription. These include the pRB family of proteins,p300/CBP and TATA binding protein. In addition to this, E1A increasesthe level of p53 protein in the cells. In the absence of adenovirus E1Bactivity, the rise in p53 levels leads to the induction of apoptosis.Both proteins encoded by the E1B region counteract the induction ofapoptosis, although by different mechanisms. E1B-21K seems to counteractapoptosis in a manner similar to Bcl-2 via interaction with the effectorproteins downstream in the apoptosis pathway (Han et al., 1996), whereasE1B-55K functions through direct interaction with p53. Importantly, themolecular mechanism by which the E1B-55K proteins of Ad2 and 5 (subgroupC) and Ad12 (subgroup A) function in the ability to neutralize p53 maydiffer. Whereas Ad5 E1B-55K binds p53 strongly and the complex localizesto the cytoplasm, Ad12-E1B-55K binds p53 weakly and both proteins arelocalized in the nucleus (Zantema et al., 1985; Grand et al., 1999).Both proteins, however, inhibit the transactivation of other genes byp53 (Yew and Berk, 1992).

In rodent cells, the activity of E1A, together with either E1B-21K or55K, is sufficient for full transformation, although expression of bothE1B proteins together is twice as efficient (Rao et al., 1992;). Inhuman cells, however, the activity of the E1B-55K protein seems to bemore important, given the observation that E1B-55K is indispensable forthe establishment of transformed cells (Gallimore, 1986).

Example 6 hereof describes the generation of pIG270. In this construct,the Ad35-E1 genes are expressed from the HPGK promoter and transcriptionis terminated by the HBVpA. The hPGK promoter constitutes a HincII-EcoRIfragment of the promoter sequence described by Singer-Sam et al. (1984).The HBVpA is located in a BamHI-BglII fragment of the Hepatitis B virusgenome (Simonsen and Levinson, 1983; see also Genbank HBV-AF090841). Asmentioned before, the promoter and polyadenylation sequences of the E1expression constructs described in this invention may be derived fromother sources without departing from the invention. Also, otherfunctional fragments of the HPGK and HBVpA sequences mentioned above maybe used.

The functionality of pIG270 was shown by transformation of primary BabyRat Kidney cells (BRK). Comparison with an equivalent Ad5-E1 expressionconstruct taught that Ad35-E1 genes were less efficient in transformingthese cells. The same has been found for the E1 genes of Ad12 (Bemardset al., 1982).

It is unclear which E1 protein(s) determine(s) the difference intransformation efficiency of E1 sequences observed for adenoviruses fromdifferent subgroups. In the case of Ad12, transfection studies withchimeric E1A/E1B genes suggested that the efficiency of transformationof BRK cells was determined by the E1A proteins (Bemards et al., 1982).The E1B-55K protein is shown infra to contain serotype-specificfunctions necessary for complementation of E1-deleted adenoviruses. Ifthese functions are related to the regulation of mRNA distribution oranother late viral function, it is unlikely that these are involved inthe transformation efficiency.

Analysis of functional domains in the Ad2 or Ad5-E1B-55K proteins usinginsertion mutants have revealed that functions related to viralreplication, late protein synthesis and host protein shut-off are notconfined to specific domains but are distributed along the protein (Yewet al., 1990). Using the same set of mutants, the domains important forinteraction with p53 and E4-Orf6 were found to be more restricted. Inaddition to one common binding region (amino acids 262 to 326), p53binding was affected by mutations at aa 180 and E4-Orf6 binding wasaffected by mutations at aa 143 (Yew and Berk, 1992; Rubenwolf et al.,1997).

Altogether, these results indicate that it is difficult to separate theE1B-55K functions related to transformation (p53 binding) and lateprotein synthesis (Orf6 binding).

The invention discloses new E1 constructs that combine the highefficiency of transformation of one serotype with the serotype-specificcomplementation function of another serotype. These new constructs areused to transform primary human embryonic retinoblast cells and humanamniocytes.

The Generation of pIG535, pIG635 and pIG735

Construct pIG535 contains the Ad5-E1A region and E1B promoter sequenceslinked to the Ad35-E1B sequences. Hereto, pIG270 (FIG. 14; see example6) was digested with EcoRI and NcoI. The 5.3 kb vector fragment was thenisolated from gel using the GENECLEAN kit (BIO Inc. 101) according tothe instructions of the manufacturer. Next, construct pIG.E1A.E1B (FIG.12; see example 6) was digested with EcoRI and XbaI and the resulting890 bp fragment was isolated as above. A third fragment was generated byPCR amplification on pIG.E1A.E1B using the following primers:

(SEQ ID NO:30) 5E1A-F: 5′-GAG ACG CCC GAC ATC ACC TG-3′ and (SEQ IDNO:31) 5E1B-R: 5′-CAA GCC TCC ATG GGG TCA GAT GTA AC-3′.The following PCR program was used: 94° C. for 2′ followed by 30 cyclesof 94° C. for 30″, 60° C. for 30″ and 72° C. for 1′, and a final step at72° C. for 10′ to ensure blunt ends.

The resulting 400 bp PCR fragment was digested with XbaI and NcoI. Aftergel isolation as above, the three fragments were ligated and transformedinto STBL-2 bacteria. One colony containing all three fragments in thecorrect order was selected and designated pIG535 (FIG. 25).

Construct pIG635 contains the Ad5-E1A and a chimeric Ad5-Ad35-E1B regionsuch that the 21K sequence is essentially from Ad5 and linked to theAd35-E1B-55K sequences as far as not overlapping with the 21K sequences.First, part of the Ad5-E1 sequences are amplified by PCR usingpIG.E1A.E1B as template and the following primers: 5AK: 5′-GAG CGA AGAAAC CCA TCT GAG-3′ (SEQ ID NO:32) and 2155R: 5′-GGT CCA GGC CGG CTC TCGG-3′ (SEQ ID NO:33). Amplification is accomplished with Pwo DNApolymerase (Roche) according to manufacturer's instructions. The 210 bpfragments are then purified from the primer sequences using the PCRpurification kit (Qiagen).

A second PCR fragment is amplified from pIG270 DNA as described abovebut with the following primers:

(SEQ ID NO:34) 2155F: 5′-CCG AGA GCC GGC CTG GAC-3′ and (SEQ ID NO:35)35F10: 5′-GCT CTA GAC CTG CAG GTT AGT CAG TTT CTT CTC CAC TG-3′.

The 1.3 kb amplified fragment is purified as above and mixed in a 1:1molar ratio with the first PCR fragment. The mixture is then firstsubjected to a PCR reaction without the addition of primers using PwoDNA polymerase and the following program: 94° C. for 2′ and then 5cycles of 94° C. for 30″, 60° C. for 30″, 72° C. for 90″. Subsequently,primers 5AK and 35F10 are added at 0.6 μm concentration after which alast PCR amplifies a 1.5 kb fragment. Hereto, temperature was set asfollows: 94° C. for 2′, then 30 cycles of 94° C. for 30″, 60° C. for 30″and 72° C. for 90″, followed by a final step at 72° C. for 10′ to ensureblunt ends. The resulting product is purified using the PCR purificationkit (Qiagen) as above and digested with KpnI and SbfI (isoschizomer ofSse83871). The digested DNA is then isolated from gel using theGENECLEAN kit (BIO Inc., 101). Construct pIG.E1A.E1B is digested withKpnI and SbfI and the vector-containing fragment is isolated from gel asabove. This fragment is ligated to the above prepared final PCR productand the ligation mixture is transformed into STBL-2 cells (Gibco, LTI)according to manufacturer's instructions. This gives construct pIG635(FIG. 26).

In construct pIG735, the border between Ad5 derived sequences and Ad35derived sequences is located more 3′ than in construct pIG635. First, aBspEI site is introduced in the Ad5 sequence of construct pIG.E1A.E1Bwithout changing the amino acid sequence. Hereto, Ad5 sequences frompIG.E1A.E1B are amplified using the following PCR primers:

5AK: see above (SEQ ID NO:32), and Bsp-R: 5′-GCT CTA GAC CTG CAG GGT AGCAAC AAT TCC GGA TAT TTA CAA G-3′ (SEQ ID NO:36). Amplification isaccomplished using Pwo DNA polymerase (Roche) according to themanufacturer's instruction. The following PCR program is used: 94° C.for 2′ followed by 30 cycles of 94° C. for 30″, 60° C. for 30″ and 72°C. for 30″, and a final step at 72° C. for 10′ to ensure blunt ends. Theresulting 0.6 kb fragment is purified as above and digested with KpnIand SbfI and ligated to the above described KpnI/SbfI digestedpIG.E1A.E1B vector fragment. Selection of colonies after transformationof STBL-2 bacteria (Life Techn. Inc.) gives construct pIG.E1Δ55K.pIG.E1Δ55K is then digested with SbfI and partially with BspEI. The 6.4kb SbfI-partial BspEI digested vector fragment is then isolated from gelusing the GENECLEAN kit (BIO 101, Inc.). Next, pIG270 is digested withBspEI and SbfI and the resulting 915 bp fragment is isolated from gel asabove. This fragment is then ligated to the above prepared SbfI/partialBspEI digested pIG.E1Δ55K vector fragment and transformed into STBL-2competent cells. This gives construct pIG735 (FIG. 27). Clones areanalyzed by restriction enzyme digestion and sequencing to ensurecorrect ligation of the fragments. Constructs pIG535, pIG635 and pIG735can be used to generate complementing cell lines from primary humancells as described in Example 6.

Example 9

PER.C6-Based Complementing Cell Lines for E1-Deleted Ad35 Viruses

PER.C6 cells were seeded in 10 cm culture dishes at a density of 3×10⁶cells/dish in DMEM (Gibco BRL) complemented with FBS (Gibco BRL) up to10% and 10 mM MgCl₂ (4.9 M stock solution, Sigma). Two days later, 9dishes were transfected with 1 μg ScaI linearized pIG35.55K DNA (seeexample 7) and 9 dishes were transfected with 1.5 μg ScaI linearizedpIG35.55K DNA. Separate control dishes were transfected with 1 or 1.5 μgScaI linearized pAdApt35.LacZ to monitor transfection efficiency andwith 1 or 1.5 μg ScaI linearized pcDNA.nlsLacZ. pcDNA.nlsLacZ is apcDNA3-based plasmid (Invitrogen) with the nlsLacZ gene (Bonnerot etal., 1987) driven by the CMV promoter. pcDNA.nlsLacZ also contains aneo^(r) expression cassette. As a negative control one extra dish wastransfected with linearized pAdApt35.LacZ, a construct that lacks theneo^(r) selection gene. All transfections were performed with theLipofectAmine transfection kit (Invitrogen/Life Technologies) accordingto manufacturers' instructions using 5 ml LipofectAmine reagent/μg DNA.Cells were incubated for 4 hrs with the transfection mixture after whichthe medium was replaced with PER.C6 culture medium. The next day mediumwas replaced with culture medium containing 0.5 mg/ml G418 (Gibco BRL)except in the two dishes that were transfected with 1 or 1.5 μgpAdApt35.LacZ. These latter dishes were used to monitor LacZ expressiontwo days following transfection. After X-gal staining of these culturestransfection efficiency was estimated at approximately 40% with slightlymore blue cells in the dish transfected with 1.5 μg DNA. Selectionmedium was refreshed twice weekly in the remaining transfected dishes.Within two weeks following first addition of selection medium most cellsin the negative control dish (transfected with 1.5 μg pAdApt35.LacZ)were dead. In the dishes transfected with pcDNA.nlsLacZ cell clones werebecoming visible. Since the cells transfected with pIG35.55K seemed tobe more resistant to G418, the concentration was raised to 0.75 mg/ml 3weeks following transfection. Three days and seven days later a total of196 cell clones were picked from the dishes transfected with pIG35.55Kand seeded in separate wells of 96-well plates.

Cells remaining after colony picking of two 10 cm dishes of thetransfection with 1 μg pIG35.55K DNA were trypsinized, pooled andexpanded to give pool PER55K(1.0) The same was done for two dishes ofthe 1.5 μg transfection. The PER55K(1.0) cell pool was expanded andseeded in 4 T25 flasks at a density of 3.5×10⁶ cells/flask fortransfection to test virus generation. In addition, 3 T25 flasks withparental PER.C6 cells were seeded at the same density. pAdApt35.eGFP (anadapter plasmid containing the green fluorescent protein as marker gene;see example 4) was digested with PacI to liberate the adenoviralsequences from the plasmid backbone. pWE.Ad35.pIX-rITR (see, example 4)was digested with NotI to liberate the adenoviral sequences from thecosmid backbone. 2 flasks with PER.C6 cells and 2 flasks withPER55K(1.0) cells were transfected with 2 μg digested pAdApt35.eGFP and6 μg digested pWE.Ad35.pIX-rITR each. One flask of each cell line wastransfected with 8 μg pAdApt35.LacZ to monitor transfection efficiency.The remaining flask with PER55K(1.0) cells served as a negative controland was treated as the others but did not receive the transfectionmixture. All transfections were performed with LipofectAmine(Invitrogen/Life Techn.) according to manufacturers' instructions usingfor each transfection a total of 8 μg DNA and 40 μl LipofectAminereagent. The transfection mixture was removed after 4 hrs incubation andfresh culture medium was added. Transfections were done the day afterseeding of the cells and again two days later cells in the T25 flaskswere transferred to a T80 flask except for the LacZ controltransfections. These were stained with X-gal solution after mildfixation. After five hours incubation with staining solution, thepercentage of blue cells was estimated at approximately 90% in bothflasks showing that transfection went well for both cell lines. Fourdays following the passage to the T80 flasks the transfected PER55K(1.0)cultures showed starting CPE (cytopathogenic effect, indicative of virusreplication) with approximately 100 events/flask. The untransfectedPER55K(1.0) cells were grown confluent with no evidence of CPE. In thetransfected PER.C6 cultures only three CPE events were visible in theconfluent monolayer of cells. Again three days later, the transfectedPER55K(1.0) cultures showed full CPE, with all cells rounded anddetached in clumbs. In contrast, in the PER.C6 cultures the few eventsof CPE had not progressed and cells were still in monolayer. Thisconfirms earlier observations that generation of E1-deleted Ad35-basedviruses on PER.C6 is very inefficient. Also the untransfectedPER55K(1.0) cultures showed, as expected, a confluent monolayer with noCPE. The cells and medium in the PER55K(1.0) flasks with full CPE wereharvested and subjected to two freeze/thaw cycles after which the celldebris was removed by centrifugation at 3000 rpm for 10 minutes in atable centrifuge. One of the resulting crude lysates was used to infecta fresh culture of PER55K(1.0) cells in a T175 flask (1.5 ml/flask).Cells and medium were harvested at full CPE four days later. This showsthat infectious virus had formed in the initial transfections. GFPexpression was confirmed by fluorescent microscopy of A549 cellsinfected with the crude lysate. The crude lysate was then used toanalyze complementation of this E1-deleted Ad35.AdApt.eGFP virus in theindividual clones as described below.

The above-described clones that were picked from the pIG35.55Ktransfected PER.C6 cells were expanded and were functionally tested forthe ability to sustain replication of Ad35.AdApt.eGFP. Hereto, theclones were seeded at two densities in 6-well plates and one day laterinfected with 15 ml of the above described crude lysate. CPE wasmonitored the day after. Of the 146 clones tested in this way 19 gavefull CPE at day 2 or 3 and 68 gave full CPE at day 5 or 6. The remainingclones had only partial CPE or showed a few non-progressing events. Thelatter were indistinguishable from PER.C6 cells that were taken along asa negative control.

Based on these results a selection of 24 clones was made that werefurther screened for the ability to generate recombinant E1-deletedviruses following transfection of the pAdApt35.GFP adapter plasmid andthe large pWE.Ad35.pLX-rITR cosmid clone. Hereto, clones were plated inT25 flasks and transfected with 2 μg of the adapter and 6 μg of thebackbone plasmid using LipofectAmine as described above. Two daysfollowing the transfection, cells were transferred to T80 flasks toprevent overconfluency of the cultures. Of the 24 clones 5 gave full CPEthree days after passage to T80 and another 13 clones gave progressingto full CPE the day after. The remaining 6 clones showed no CPE or onlystarting. In comparison: routine generation of E1-deleted Ad5 vectors onPER.C6 cells generally results in full CPE four to six days aftertransfer to T80 flasks.

This shows that the new clones efficiently complement E1-deletedadenovirus vectors. One of the clones (clone #16) described above wasused to generate and produce multiple batches of E1 and E1/E3 deletedAd35 viruses containing different transgenes. Hereto, virus in crudelysates resulting from transfections as described above, but usingdifferent adapter plasmids, were plaque purified on the new cell line.Single plaques were tested for transgene activity and then amplified formedium scale production in 4-8 triple layer flasks (3×175 cm/flask).Cells were harvested at full CPE and the virus was released and purifiedas routinely done for adenoviruses and described in example 1. Theextraction step with freon to remove cellular debris was, however,replaced by a centrifugation step. Thus after incubation with Dnasel,the cell debris was centrifugated in conical 50 ml tubes (Greiner) at8000 rpm in a table top centrifuge (Beckman Coulter Allegra 21R withfixed angle rotor) for 30 minutes at 4° C. This step is repeated in afresh 50 ml tube until the supernatant was clear (usually one time). Theamount of virus particles was determined by HPLC (Shabram et al., 1997).Table IV presents the yields after downstream processing of medium scaleproductions of E1- and E1/E3-deleted Ad35 viruses on triple layer flaskswith PER55K clone #16 cells. The amount of purified virus particles iscomparable with the yields of Ad5-based vectors on PER.C6 cells.

We conclude that we have generated multiple cell lines that efficientlycomplement fully E1-deleted Ad35-based vectors. Thus, Ad35 E1B-55Kexpression in an Ad5 complementing cell line facilitates replication ofAd35 vectors.

Example 10

New Complementing Cell Lines from Primary Cells

Example 8 described the generation of construct pIG535, a hybridAd5E1A-Ad35 E1B expression plasmid. pCC536s and pIG536 are also hybridAd5-Ad35 E1 constructs but with the E1A region, E1B promoter and most ofthe E1B-19K gene derived from Ad5 and most of the E1B-55K gene derivedfrom Ad35. Constructs pCC536s and pIG536 differ only in the heterologouspoly adenylation sequence that terminates the E1B transcript: pIG536 hasthe HBV pA sequence and pCC536s has a synthetic pA sequence (SpA). TheSpA sequence consists of the upstream sequence element (USE) of thehuman C2 complement gene (Moreira et al., 1995) and the synthetic pAsequence (SPA) described by Levitt et al., 1989.

The synthetic polyA sequence is build up using the following oligos:

(SEQ ID NO:37) C2SPA-1: 5′-CCC TGC AGG GAC TTG ACT CAT GCT TGT TTC ACTTTC ACA TGG AAT TTC CCA GTT ATG AAA TTA ATA AAG-3′ and (SEQ ID NO:38)C2SPA-2: 5′-GTC TAG ACA CAC AAA AAA CCA ACA CAC TAT TGC AAT GAA AAT AAATTT CCT TTA TTA ATT TCA TAA CTG-3′.Oligonucleotides were mixed at 10 μM concentration in 1× annealingbuffer (10 mM Tris HCl pH 7.5, 100 mM NaCl, 1 mM EDTA) and, using a PCRmachine, the solution was heated to 94° C. for 5 minutes and then cooleddown to 65° C. at 0.5° C./second and after incubation at 65° C. for 5minutes further cooled down to 20° C. at 0.05° C./second. Subsequently,10 μl 2 mM dNTPs, 0.5 μl 1M MgCl2 and 3 μl Klenow fragment (New EnglandBiolabs) was added to 87 μl of the annealed sample and the mixture wasincubated at room temperature for 30 minutes. 1 μl of the annealed andKlenow treated sample was then amplified using the following primers:C2for: 5′-CGG GAT CCC CTG CAG GGA CTT GAC-3′ (SEQ ID NO:39) and SPArev:5′-TTG CGA CTT AAG TCT AGA CAC ACA AAA AAC C-3′ (SEQ ID NO:40) using PwoDNA polymerase (Roche) according to manufacturers instructions but withaddition of DMSO (Sigma) to a final concentration of 3%. The PCR programwas set at 94° C. for 2 minutes, followed by 30 cycles of (94° C. for30″, 55° C. for 30″ and 72° C. for 20″). Where in this document PCRprograms are described “means time in minutes and” “means time inseconds.” The amplified DNA was then purified using the QIAquick PCRpurification kit (Qiagen) and digested with XbaI and SbfI. The digestedproduct was then again purified with the PCR purification kit to removethe small digested ends. Construct pIG270 was also digested with XbaIand SbfI (isoschizomer of Sse8387I) and the resulting 5.9 kb vectorcontaining fragment was isolated from gel using the GeneClean II kit(BIO 101, Inc). The treated vector and PCR insert were then ligated togive pCC271 (FIG. 28). pCC271 thus contains the PGK promoter, the Ad35E1 region (nucl. 468 to and including 3400 from Ad35 sequence in example3 and SEQ ID NO:44) and the synthetic pA (SpA). The synthetic pAsequence was then also cloned into the construct pIG535 as follows.

pIG535 was digested with EcoRI, PstI and ScaI (All enzymes from NewEngland Biolabs digested in NEB buffer 3) and the 3 kb insertcorresponding to chimeric Ad5-Ad35 E1 region was purified using theGeneClean II kit (BIO 101, Inc.). Construct pCC271 was digested withEcoRI and PstI and the 3 kb vector fragment containing the SpA and PGKpromoter was isolated as above. Both isolated fragments were ligated andtransformed into STBL-2 competent cells (Invitrogen/LifeTechnologies) togive pCC535s (FIG. 29). pCC535s contains the same Ad5-Ad35 E1 sequencesas pIG535 however, a different pA sequence.

For the construction of pCC536s, a subclone was made with the new hybridE1B sequences. Hereto, Ad5 E1A/E1B21K sequences were amplified using theprimers 5AK: 5′-GAG CGA AGA AAC CCA TCT GAG-3′ (SEQ ID NO:32) and 2155R:5′-GGT CCA GGC CGG CTC TCG G-3′ (SEQ ID NO:33) with pIG.E1A.E1B (see,example 6 and FIG. 12) as template DNA using Pwo DNA polymerase (Roche)according to manufacturers instructions and in addition a finalconcentration of 3% DMSO. The program was set at: 94° C. for 2′ followedby 30 cycles of (94° C. for 30″, 58° C. for 30″ and 72° C. for 30″) andended with 68° C. for 8′. This resulted in a 210 bp fragmentcorresponding to nucl. 2022-2233 of the Ad5 sequence. A second PCR wasperformed on pCC271 with primers

(SEQ ID NO:41) 2155F: 5′-CCG AGA GGC GGC CTG GAG C-3′ and (SEQ ID NO:21)35F10: 5′-GCT CTA GAC CTG CAG GTT AGT CAG TTT CTT CTC CAC TG-3′.

The same PCR program was used but now with an elongation time of 90″.The resulting 1.3 kb fragment corresponds to nucl. 2112 to 3400 of theAd35 sequence with an SbfI site at the 3′end. Note that primers 2155F(SEQ ID NO:41) and 2155R (SEQ ID NO:33) are fully complementary allowingassembly of the two fragments as follows:

Both PCR fragments were purified from gel using the Qiagen gelextraction kit. Aliquots of the purified samples were then mixed inequimolar ratio and used as template for an assembly PCR amplificationwith primers 5AK (SEQ ID NO:32) and 35F10 (SEQ ID NO:21) with Pwo DNApolymerase as above using the program settings: 94° C. for 2′, and 5cycles of (94° C. for 30″, 60° C. for 30″ and 72° C. for 2′) followed by25 cycles of (94° C. for 30″, 58° C. for 30″ and 72° C. for 90″). Theresulting 1.5 kb fragment was purified from gel using the QIAquick gelextraction kit (Qiagen), ligated to the pCR-Script/Amp cloning vector(Stratagene) and transformed into DH5a competent cells (Invitrogen/LifeTechnologies) resulting in pCR535E1B (FIG. 30). This construct waschecked by restriction analysis and sequencing to confirm correctamplification of target sequences.

pCR535E1B was then digested with NotI and protruding ends were madeblunt with Klenow fragment. The DNA was then purified using the QIAquickPCR purification kit (Qiagen) and eluted DNA was digested with PstI. The1.5 kb fragment containing the chimeric E1 sequences from the pCR535E1Bvector was purified from gel using the GeneClean II kit (BIO 101, Inc.).This fragment was ligated to vector pCC535s digested with PvuII andPstI, and transformed into STBL-2 competent cells (Invitrogen/LifeTechnologies) to give pCC2155s (FIG. 31). To complete the pCC536sconstruct Ad5-E1 sequences were then cloned into the pCC2155s subclone.Hereto, pIG.E1A.E1B was digested with EcoRI and KpnI and the 1.6 kbfragment corresponding to Ad5 E1A and Ad5 E1B 21K (nucl. 459 to 2048 ofthe Ad5 sequence) was isolated from gel using the GeneClean kit.pCC2155s was digested with EcoRI and KpnI and the vector containingfragment was also gel purified. Ligation of both isolated fragments andtransformation into DH10B electrocompetent cells (Invitrogen/LifeTechnologies) resulted in pCC536s (FIG. 32). The hybrid E1B sequencesare shown in FIG. 37 in more detail. FIG. 37A shows an alignment ofprotein sequences of E1B-21K in the pCC536s construct with wild type(wt) Ad35 and Ad5 sequences. As can be seen most of the E1B-21K proteinin pCC536s is derived from Ad5 except for the C-terminal 6 amino acidsthat are identical to Ad35 E1B-21K. FIG. 37B shows the same alignmentfor the E1B-55K proteins. In this case the N-terminal amino acids ofpCC536s are identical to Ad5 upto aa 65. The remainder is identical toAd35 E1B-55K. Obviously, different hybrid E1B-55K constructs can bedesigned using the general method outlined above without departing fromthe invention.

Construct pIG536 was made by replacing a fragment with the SpA inpCC536s with the corresponding fragment from pIG270 (example 6, FIG. 14)containing the HBVpA. Hereto, pIG270 was digested with BamHI and BglIand the 1.8 kb insert was isolated from gel using the GeneClean II kit(BIO 101, Inc.). pCC536s was digested with the same enzymes and the 4.8kb vector containing fragment was purified from gel as above. Ligationof both isolated fragments and transformation into STBL-2 competentcells (Invitrogen/Life Technologies) gave construct pIG536 (FIG. 33).

The generated E1 constructs were tested in primary baby rat kidney (BRK)cells as described in example 6. The results (Table V) confirm earlierobservations that Ad5-E1 genes more efficiently transform primary BRKcells than Ad35 E1 genes. The chimeric Ad5-Ad35 E1 expressionconstructs, pCC535s and pCC536s, produced more transformed colonies thanthe full Ad35 E1 constructs, pIG270 and pCC271. Furthermore, the use ofa synthetic poly adenylation sequence in pCC535s resulted in slightlymore foci compared to the HBVpA variant pIG535.

Human embryonic retinoblast (HER) cells were isolated from the eyes ofaborted fetuses of 18 and 21 weeks of age. The eyes were brought in a 6cm dish with PBS and cleared from outside tissue. An incision was madeto reach the inner side and the gray cell layer at the inner back of theeyes containing the retinoblasts, was scraped off. This layer wastransferred to a 14 ml tube in 2 ml of PBS and tissue was allowed tosediment after which the PBS was removed. 2 ml trypsin (0.25%, no EDTA,GibcoBRL) was added and incubated for 5 minutes at 37° C. withoccasional swirling. Tissue pieces were allowed to sediment and 1 mltrypsin with cells was transferred to a new tube. To this tube 4 mlculture medium (DMEM with 10% FCS) was added and the tube was stored onice. The remaining tissue pieces in trypsin were brought in a 6 cm dishand cut into smaller pieces. These were, after addition of 2 ml freshtrypsin, again incubated in a 14 ml tube at 37° C. with occasionallyswirling. Then this mixture was added to the first isolated cells inculture medium and the total was centrifugated at 1000 rpm in a tabletop centrifuge. Supernatant was removed and cells were resuspended in 10ml of culture medium. The isolated HER cells were plated in two 6 cmdishes and incubated at 37° C./10% CO₂. Upon 90% confluency cultureswere split 1:3 and further incubated. This procedure was repeated untilenough dishes were obtained to be used for transfection and furtherculturing. Transfections were performed at different passage numbersusing the CaPO₄ cotransfection kit (Invitrogen/Life Technologies)according to manufacturers instructions. For each dish (50-70%confluency) 20 μg DNA was used. Initial transfections were performedwith pIG.E1A.E1B, an Ad5-E1 expression construct, and with pIG535, thehybrid Ad5-E1A/Ad35-E1B expression construct. 2-3 weeks followingtransfection transformed foci became visible in the pIG.E1A.E1Btransfected dishes. On average 15-20 foci/dish were found in the dishesthat were transfected with pIG.E1A.E1B. Over 30 clones were picked andtransferred to 96-well plates. Upon confluency cells were passaged tolarger culture plates or flasks and finally viable frozen in ampoules inliqN₂ from a T175 flask. All picked clones were established in this way.Transformed foci appeared much later in the dishes that were transfectedwith pIG535, the first around five weeks following transfection. Onaverage 3-4 clones were found per dish. A total of 46 clones were pickedfrom 7 weeks to 3 months after transfections of which 14 were viable andcould be passaged multiple times. Of these, 2 clones (clone #45 and #75)were grown up to a T175 flask and viable frozen in ampoules in liqN₂.

Primary HER cells were also transfected with constructs pCC535s andpCC536s. Transfection of pCC535s let to an average of 2 clones/dish anda total of 50 clones were picked. Of these picked clones 2 could beestablished. From the transfection with pCC536s, at least one clonecould be established.

The above-described experiments show that primary HER cells can betransformed with hybrid Ad5-Ad35E1 sequences. The efficiency oftransformation was lower than obtained with the complete Ad5 E1 region.We then tested whether the new cell lines could complement recombinantAd35-based E1-deleted vectors. Hereto, the clone #45 that was obtainedfrom the pIG535 transfection was seeded in T25 flasks at a density of7×10⁶ cells/flask and infected with Ad35.AdApt.eGFP virus (see example9) at a multiplicity of infection (moi) of 5 and 25 virusparticles/cell. Full CPE was seen at days 4 and 5 for the moi 25 and 5respectively. As a comparison parallel cultures of clone #45 cells thatwere infected with Ad5.AdApt.eGFP viruses gave full CPE at days 7 and 8for moi 25 and 5, respectively. The initial infection efficiency wascomparable for Ad5 and Ad35 viruses, ˜80% (moi=5) and 95% (moi=25) ofthe cells were infected with GFP virus one day following infection asmeasured by fluorescence microscopy. Cells from clone #75 were seeded ina 6-well plate at a density of 2×10⁶ cells/well and infected withAd35.AdApt.eGFP or Ad5.AdApt.eGFP at moi 5 (VP/cell). Again initialinfection efficiency was comparable for both viruses. Full CPE wasobserved at day 4 in case of Ad35.AdApt.eGFP infection whereasAd5.AdApt.eGFP infected clone #75 cells gave full CPE on day 7. Thedifference in replication efficiency on Ad35 complementing cells betweenAd35 and Ad5 recombinant vectors is even more clear when virus isgenerated by plasmid transfection. This is exemplified by the followingtransfection experiment. Clone #45 cells were seeded in T25 flasks at adensity of 3.5×10⁶ cells and transfected three days later usingLipofectAmine reagent (Invitrogen/Life Technologies) according tomanufacturers instructions and described above. 2 μg pAdApt35.eGFPadapter plasmid digested with PacI was cotransfected with 6 μgpWE.Ad35.pIX-ITR or pWE.Ad35.pLX-rITRΔE3 backbone cosmid digested withNotI. 2 μg pAdApt.eGFP (Ad5 adapter plasmid, described in WO 00/70071)digested with PacI was cotransfected with 6 μg pWE.Ad5.AflII-rITRsp (Ad5backbone plasmid, described in WO 00/70071) also digested with PacI. OneT25 was not transfected and served as a negative control. One day latertransfection efficiencies were monitored by fluorescent microscopy andestimated at 10-15% in all eGFP transfections. Three days followingtransfection cells were transferred to T80 flasks and further incubatedat 37° C./10% CO₂. Again three days later CPE events were becomingvisible in the cultures transfected with the pAdApt35.eGFP and thepWE.Ad35pIX-rITR+ or −E3. The transfections with the E3-deleted backbonecontained more green fluorescent cells and more CPE events. Thetransfection with Ad5 plasmids showed only around 20% green fluorescentcells, of which most were dying, and no CPE events. Two days later thisdifference had become bigger since cultures transfected with thepAdApt35.eGFP and the pWE.Ad35pIX-ITRΔE3 clearly showed 80% CPE andcultures transfected with the pAdApt35.eGFP and the pWE.Ad35pIX-rITRconstructs showed progressing CPE events. The Ad5 transfected culturedid not show any progression. Table VI summarizes these results.

We conclude that the new complementing cell lines described aboveefficiently sustain replication of E1 deleted Ad35-based viruses andthat the generation and replication of E1 deleted Ad5-based viruses isless efficient. Apparently, also Ad35-E1B55K proteins do not form afunctional complex with Ad5-E4Orf6 proteins. Thus the serotypespecificity for complementation is now also shown for recombinant Ad5vectors on Ad35 packaging cells.

Example 11

Generation of pWE.Ad.pIX-rITRΔE3

The early region-3 of human adenoviruses contains multiple codingregions for proteins that interfere with the host immune response toadenoviral infection. When adenoviral vectors are used as vaccinecarrier such interference is unwanted. Therefore, we constructed an Ad35backbone cosmid lacking the E3 region.

Hereto, construct pBr.Ad35.PRn (FIG. 34; described in example 13 inpublication EP 1 054 064 A1) was digested with StuI and MluI and the17.3 kb vector fragment was purified from low melting point (LMP) gelusing agarase enzyme (Roche) according to manufacturers instructions.Next, a PCR fragment was generated on pBr.Ad35.PRn using primers:35E3for: 5′-AAT GAC TAA TGC AGG TGC GC-3′ (SEQ ID NO:42) and 35E3rev:5′-CGA CGC GTT GTA GTC GTT GAG CTT CTA G-3′ (SEQ ID NO:43). For theamplification Pwo DNA polymerase (Roche) was used according tomanufacturers instructions and program set at: 94° C. for 2′, 30 cyclesof (94° C. for 30″, 58° C. for 30′″ and 72° C. for 1′) and a finalincubation at 68° C. for 8′. The 833 bp PCR product was purified usingthe QIAquick PCR purification kit (Qiagen) and digested with MluI andStul. The digested DNA was purified from gel using the QIAquick gelextraction kit (Qiagen). Both isolated fragments were ligated andtransformed into DH5a competent cells (Invitrogen/Life Technologies) togive pBr.Ad35.PRnΔE3 (FIG. 35). The plasmid was checked by restrictionanalysis and sequencing of the PCR amplified insert. The E3 deletion wasthen cloned into the pWE.Ad35.pIX-rITR cosmid backbone. Hereto,pWE.Ad35.pIX-rITR (see example 4 and FIG. 7) was digested with PacI andthe DNA was purified by precipitation with isopropanol and washing with70% EtOH. Following resuspension in milliQ water, the DNA was digestedwith SwaI and the 22.8 kb vector containing fragment was purified fromLMP gel using agarase enzyme as above. Construct pBr.Ad35.PRnΔE3 wasdigested with PacI and SwaI in the same manner and the 16.6 kb fragmentwas also isolated using agarase enzyme. Both isolated fragments wereligated using 0.5-0.6 μg of each fragment. Ligated fragments were thenpackaged using λ-phage packaging extracts (Stratagene) according tomanufacturers instructions and mixed with STBL-2 cells. Bacteria wereplated on LB+Amp plates and resulting colonies were analyzed for thepresence of the correct construct. This gave constructpWE.Ad35.pIX-rITRΔE3 (FIG. 36). The E3 deletion extends from nucl. 27648to 30320 of the Ad35 sequence (example 3) and thus spans a 2.6 kbregion.

Cotransfection of NotI digested pWE.Ad35.pIX-rITRΔE3 and pIPsp-1digested pAdApt35.eGFP onto PER55-clone #16 cells (see example 9) asdescribed above gave rise to GFP expressing Ad35-based viruses. Uponisolation of viral DNA from these viruses, PCR amplification of the E3region showed that the viruses were deleted for 2.6 kb of E3 sequencesas expected.

TABLE I Elution log₁₀ VP/CCID50 Serotype [NaCl] mM VP/ml CCID50 ratio 1597 8.66 × 10¹⁰ 5.00 × 10⁷ 3.2 2 574 1.04 × 10¹²  3.66 × 10¹¹ 0.4 3 1311.19 × 10¹¹ 1.28 × 10⁷ 4.0 4 260 4.84 × 10¹¹ 2.50 × 10⁸ 3.3 5 533 5.40 ×10¹¹  1.12 × 10¹⁰ 1.7 6 477 1.05 × 10¹²  2.14 × 10¹⁰ 1.7 7 328 1.68 ×10¹² 2.73 × 10⁹ 2.4 9 379 4.99 × 10¹¹ 3.75 × 10⁷ 4.1 10 387 8.32 × 10¹²1.12 × 10⁹ 3.9 12 305 3.64 × 10¹¹ 1.46 × 10⁷ 4.4 13 231 4.37 × 10¹² 7.31× 10⁸ 3.8 15 443 5.33 × 10¹² 1.25 × 10⁹ 3.6 16 312 1.75 × 10¹² 5.59 ×10⁸ 3.5 17 478 1.39 × 10¹² 1.45 × 10⁹ 3.0 19 430 8.44 × 10¹¹ 8.55 × 10⁷4.0 20 156 1.41 × 10¹¹ 1.68 × 10⁷ 3.9 21 437 3.21 × 10¹¹ 1.12 × 10⁸ 3.522 365 1.43 × 10¹² 5.59 × 10⁷ 3.4 23 132 2.33 × 10¹¹ 1.57 × 10⁷ 4.2 24405 5.12 × 10¹² 4.27 × 10⁸ 4.1 25 405 7.24 × 10¹¹ 5.59 × 10⁷ 4.1 26 3561.13 × 10¹² 1.12 × 10⁸ 4.0 27 342 2.00 × 10¹² 1.28 × 10⁸ 4.2 28 347 2.77× 10¹² 5.00 × 10⁷ 4.7 29 386 2.78 × 10¹¹ 2.00 × 10⁷ 4.1 30 409 1.33 ×10¹² 5.59 × 10⁸ 3.4 31 303 8.48 × 10¹⁰ 2.19 × 10⁷ 3.6 33 302 1.02 × 10¹²1.12 × 10⁷ 5.0 34 425 1.08 × 10¹²  1.63 × 10¹¹ 0.8 35 446 3.26 × 10¹² 1.25 × 10¹¹ 1.4 36 325 9.26 × 10¹² 3.62 × 10⁹ 3.4 37 257 5.86 × 10¹² 2.8 × 10⁹ 3.3 38 337 3.61 × 10¹² 5.59 × 10⁷ 4.8 39 241 3.34 × 10¹¹ 1.17× 10⁷ 4.5 42 370 1.95 × 10¹² 1.12 × 10⁸ 4.2 43 284 2.42 × 10¹² 1.81 ×10⁸ 4.1 44 295 8.45 × 10¹¹ 2.00 × 10⁷ 4.6 45 283 5.20 × 10¹¹ 2.99 × 10⁷4.2 46 282 9.73 × 10¹² 2.50 × 10⁸ 4.6 47 271 5.69 × 10¹¹ 3.42 × 10⁷ 4.248 264 1.68 × 10¹² 9.56 × 10⁸ 3.3 49 332 2.20 × 10¹² 8.55 × 10⁷ 4.4 50459 7.38 × 10¹² 2.80 × 10⁹ 3.4 51 450 8.41 × 10¹¹ 1.88 × 10⁸ 3.7Legend to Table I:

All human adenoviruses used in the neutralization experiments wereproduced on PER.C6 cells (Fallaux et al., 1998) and purified on CsCl asdescribed in example 1. The NaCl concentration at which the differentserotypes eluted from the HPLC column is shown. Virus particles/ml(VP/ml) were calculated from an Ad5 standard. The titer in theexperiment (CCID50) was determined on PER.C6 cells as described inExample 1 by titrations performed in parallel with the neutralizationexperiment. The CCID50 is shown for the 44 viruses used in this studyand reflects the dilution of the virus needed to obtain CPE in 50% ofthe wells after 5 days. The ratio of VP/CCID50 is depicted in log₁₀ andis a measurement of the infectivity of the different batches on PER.C6cells.

TABLE II AdApt35.LacZ viruses escape neutralization by human serum.Human serum dilution no Virus serum 10× 50× 250× 1250× 6250× AdApt5.LacZ100% 0% 0% 1% 40% 80% moi: 5 VP/cell AdApt35.LacZ 100% 100%  100%  100% 100%  100%  250 μl crude lysate

TABLE III The numbers of foci obtained with the different E1 expressionconstructs in BRK transformation experiments. Average # of foci/dish:Construct 1 μgr 5 μgr Experiment 1 pIG.E1A.E1B nd 60 pIG.E1A.E1B nd 35pRSVAd35E1 0 3 pIG.Ad35.E1 3 7 Experiment 2 pIG.E1A.E1B 37 ndpIG.Ad35.E1 nd 2 Experiment 3 pIG.E1A.E1B nd 140 pIG.Ad35.E1 nd 20pIG270 nd 30

TABLE IV Yields of E1- and E1/E3- deleted Ad35 viruses on clone #16cells produced on triple layer flasks. Scale(T175III Total # of VirusVP/ Virus flasks) Particles after DSP cell Ad35.AdApt.eGFP 4 7.5 × 10¹¹2500 Ad35.ΔE3.AdApt.empty 8   2 × 10¹² 3300 Ad35.ΔE3.AdApt.LacZ 8 3.8 ×10¹¹ 600 Ad35.ΔE3.AdApt.MV-F 4 8.8 × 10¹¹ 2900 Ad35.ΔE3.AdApt.MV-H 8 2.6× 10¹² 4250

TABLE V Transformation efficiencies on BRK cells with different Ad-E1expression constructs. Construct Transfected DNA (μg) # foci per dishExperiment 1 pIG.E1A.E1B 5 44 pIG270 5 0 pCC271 5 0 pIG535 5 1 pCC535s 52.5 Experiment 2 pIG.E1A.E1B 4 15 pCC271 4 0 pCC535s 4 3 pCC536s 4 3

TABLE VI Generation of recombinant Ad35 viruses on the new establishedcomplementing cell line clone #45. Transfected constructs Day 1 Day 3Day 6 Day 8 GFP Expression x pAdApt35.eGFP + 15%  20%  30%  50% pWE.Ad35.pIX-rITR pAdApt35.eGFP + 10%  25%  40-50%   100% pWE.Ad35.pIX-rITRΔE3 pAdApt5.eGFP + 15%  25%  20%  20% pWE.Ad5.AflII-rITR untransfected 0% 0% 0% 0% CPE events xpAdApt35.eGFP + 0  0  1  several pWE.Ad35.pIX-rITR pAdApt35.eGFP + 0  0 several 80%  pWE.Ad35.pIX- rITRΔE3 pAdApt5.eGFP + 0  0  0  0 pWE.Ad5.AflII-rITR untransfected 0  0  0  0 

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1. A packaging cell line capable of complementing a recombinantadenovirus based on a serotype from subgroup B said recombinantadenovirus lacking a functional E1 region, wherein said packaging cellline comprises functional E1A and E1B-21K coding sequences, and whereinsaid packaging cell line further comprises a functional E1B-55K codingsequence of a serotype from subgroup B, wherein at least one of the E1coding sequence is driven by a non-adenoviral promoter.
 2. The packagingcell line of claim 1, wherein said functional E1B-55K coding seciuenceis of adenovirus type
 35. 3. The packaging cell line of claim 1, whereinsaid packaging cell line comprises primary, diploid human cells, saidprimary, diploid human cells having been transformed by said E1A,E1B-21K and E1B-55K coding sequences that are either operatively linkedon one DNA molecule or located on two separate DNA molecules, said E1A,E1B-21K and E1B-55K coding sequences being operatively linked toregulatory sequences enabling transcription and translation of encodedproteins.
 4. The packaging cell line of claim 3, wherein the primary,diploid human cells have been selected from the group consisting ofprimary human retinoblasts, primary human embryonic kidney cells andprimary human amniocytes.
 5. The packaging cell line of claim 4, whereinthe primary, diploid human cells have been transformed with a chimericadenovirus E1 construct comprising said functional E1A and E1B-21Kcoding sequences, wherein said functional E1A and E1B-21K codingsequences are of a first adenovirus serotype that enables efficienttransformation of primary human cells; and said functional E1B-55Kcoding sequence of a serotype from subgroup B, wherein said functionalE1B-55K coding sequence of a serotype from subgroup B is of a secondadenovirus serotype, and wherein said functional E1B-55K coding sequenceof a serotype from subgroup B provides the serotype-specific adenovirusE1B function(s) that enable(s) efficient propagation of recombinantadenovirus E1-deleted viruses of said second adenovirus serotype.
 6. Thepackaging cell line of claim 5, wherein said first adenovirus serotypeis a subgroup C adenovirus and said second adenovirus serotype isadenovirus type
 35. 7. The packaging cell line of claim 5, wherein saidE1A coding sequence and at least part of the E1B-21K coding sequence arefrom a subgroup C adenovirus, and the E1B-55K coding sequence as far asnot overlapping with the E1B 21K coding sequence is from a adenovirusserotype
 35. 8. The packaging cell line of claim 5, wherein said E1A,E1B-21K and E1B-55K coding sequences are from a subgroup C adenovirus,except for at least a part of the E1B-55K coding sequence of a serotypefrom subgroup B that is necessary for serotype-specific complementationof an alternative adenovirus serotype, said E1B-55K coding sequence of aserotype from subgroup B being from said alternative adenovirusserotype.
 9. The packaging cell line of claim 4, wherein said cells areprimary human retinoblasts, referred to as PER.C6 cells (ECACC depositnumber 96022940) which further comprise an Ad35-E1region integrated intotheir genome, and wherein said Ad35-E1region is present in a functionalexpression cassette.
 10. The packaging cell line of claim 9, whereinsaid Ad35-E1 region does not contain sequences overlapping withsequences present in an associated recombinant viral vector.
 11. Thepackaging cell line of claim 9, wherein said functional expressioncassette comprises a heterologous promoter and a poly-adenylation signalfunctionally linked to said Ad35-E1 region, wherein said heterologouspromoter is a human phosphoglycerate gene promoter (hPGK) and whereinsaid poly-adenylation signal is a hepatitis B virus poly-adenylationsignal (HBV-pA).
 12. A PER.C6 (ECACC deposit number 96022940) cell line,comprising an Ad35-E1B coding sequence.
 13. The cell line of claim 12,wherein said Ad35-E1B coding sequence is driven by an E1B promoter andterminated by a heterologous poly-adenylation signal.
 14. The cell lineof claim 12, wherein said Ad35-E1B coding sequences is driven by aheterologous promoter.
 15. The cell line of claim 14, wherein saidAd35-E1B coding sequence is driven by an hPGK promoter or an ElongationFactor-1α (EF-1α) promoter and terminated by a heterologouspoly-adenylation signal.